Correlation between copy number variation genes and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1JS9NNR
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1JS9NNR
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 79 peak regions and 10 molecular subtypes across 358 patients, 87 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1p34.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 2(1q21.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 3(2p16.1) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Amp Peak 4(2q31.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 6(3q26.33) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 8(5p15.33) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 9(5p12) cnvs correlated to 'CN_CNMF'.

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

  • Amp Peak 18(12p13.33) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 22(15q26.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 23(17q25.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 24(18p11.32) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 25(18q11.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 26(19q12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 28(20p12.2) cnvs correlated to 'CN_CNMF'.

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

  • Del Peak 2(1p13.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 4(2q22.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 5(2q36.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 7(3p13) cnvs correlated to 'CN_CNMF'.

  • Del Peak 8(3p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 9(4p15.31) cnvs correlated to 'CN_CNMF'.

  • Del Peak 11(4q32.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 12(4q35.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 13(5q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 14(5q31.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 20(9p23) cnvs correlated to 'CN_CNMF'.

  • Del Peak 21(9p21.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 22(9q21.11) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 24(10q23.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 25(11p15.5) cnvs correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

  • Del Peak 36(17q11.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 39(19p13.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 40(19q13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 41(19q13.43) cnvs correlated to 'CN_CNMF'.

  • Del Peak 43(21q22.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 45(Xp22.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 46(Xp21.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 47(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 48(Xq22.3) cnvs correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 87 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
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
Del Peak 22(9q21 11) 174 (49%) 184 0.000177
(0.127) 		4.92e-05
(0.0363) 		2.03e-07
(0.000157) 		1.42e-06
(0.00108) 		0.571
(1.00) 		0.24
(1.00) 		4.44e-06
(0.00337) 		2.4e-07
(0.000185) 		0.0445
(1.00) 		3.16e-05
(0.0235)
Amp Peak 6(3q26 33) 330 (92%) 28 0.000427
(0.299) 		1.71e-05
(0.0129) 		1.63e-09
(1.27e-06) 		0.000113
(0.0818) 		0.213
(1.00) 		0.0944
(1.00) 		3.81e-05
(0.0283) 		0.000164
(0.118) 		0.205
(1.00) 		9.11e-05
(0.0662)
Del Peak 1(1p36 32) 155 (43%) 203 1.28e-06
(0.000976) 		1.29e-08
(1e-05) 		3.34e-28
(2.64e-25) 		4.78e-16
(3.77e-13) 		0.419
(1.00) 		0.00421
(1.00) 		1.02e-10
(8.04e-08) 		6.75e-09
(5.26e-06) 		0.0237
(1.00) 		0.00103
(0.699)
Del Peak 5(2q36 2) 116 (32%) 242 0.000236
(0.168) 		4.76e-05
(0.0352) 		5.32e-12
(4.19e-09) 		0.000352
(0.248) 		0.138
(1.00) 		0.113
(1.00) 		8.49e-05
(0.0619) 		6.15e-06
(0.00466) 		0.944
(1.00) 		0.624
(1.00)
Del Peak 2(1p13 2) 156 (44%) 202 0.000237
(0.169) 		0.00055
(0.382) 		6.47e-14
(5.1e-11) 		6.52e-09
(5.09e-06) 		0.107
(1.00) 		0.115
(1.00) 		2.35e-05
(0.0175) 		7.07e-05
(0.0517) 		0.196
(1.00) 		0.00967
(1.00)
Del Peak 36(17q11 2) 89 (25%) 269 1.26e-05
(0.00949) 		6.44e-05
(0.0473) 		9.35e-09
(7.27e-06) 		0.0579
(1.00) 		0.45
(1.00) 		0.577
(1.00) 		0.000122
(0.0881) 		7.16e-06
(0.00542) 		0.406
(1.00) 		0.0154
(1.00)
Amp Peak 3(2p16 1) 194 (54%) 164 0.000305
(0.215) 		0.00165
(1.00) 		2.41e-09
(1.88e-06) 		7e-05
(0.0513) 		0.967
(1.00) 		0.741
(1.00) 		0.000333
(0.235) 		0.00113
(0.764) 		0.879
(1.00) 		0.0312
(1.00)
Del Peak 24(10q23 31) 184 (51%) 174 0.0392
(1.00) 		0.00386
(1.00) 		0.00019
(0.136) 		6.42e-05
(0.0472) 		0.283
(1.00) 		0.303
(1.00) 		0.000104
(0.0752) 		2.63e-05
(0.0196) 		0.46
(1.00) 		0.0277
(1.00)
Amp Peak 22(15q26 3) 128 (36%) 230 0.151
(1.00) 		0.021
(1.00) 		5.63e-07
(0.000433) 		1.78e-05
(0.0134) 		0.312
(1.00) 		0.0162
(1.00) 		0.000622
(0.429) 		0.00426
(1.00) 		0.0175
(1.00) 		7.14e-05
(0.0521)
Del Peak 13(5q11 2) 265 (74%) 93 0.842
(1.00) 		0.303
(1.00) 		5.71e-10
(4.47e-07) 		0.000266
(0.188) 		1
(1.00) 		0.237
(1.00) 		0.248
(1.00) 		0.56
(1.00) 		0.888
(1.00) 		0.000162
(0.116)
Amp Peak 4(2q31 2) 121 (34%) 237 0.0207
(1.00) 		0.000948
(0.643) 		6.74e-05
(0.0494) 		4.94e-06
(0.00375) 		0.738
(1.00) 		0.912
(1.00) 		0.000801
(0.548) 		0.000932
(0.633) 		0.465
(1.00) 		0.252
(1.00)
Amp Peak 12(7q21 2) 188 (53%) 170 0.101
(1.00) 		0.25
(1.00) 		3.36e-10
(2.64e-07) 		8.35e-06
(0.00631) 		0.0408
(1.00) 		0.215
(1.00) 		0.0165
(1.00) 		0.0221
(1.00) 		0.247
(1.00) 		0.0377
(1.00)
Amp Peak 23(17q25 1) 171 (48%) 187 0.0177
(1.00) 		0.0608
(1.00) 		1.87e-06
(0.00143) 		0.000148
(0.107) 		0.297
(1.00) 		0.323
(1.00) 		0.0274
(1.00) 		0.00807
(1.00) 		0.756
(1.00) 		0.742
(1.00)
Del Peak 8(3p12 1) 280 (78%) 78 0.322
(1.00) 		0.0413
(1.00) 		1.46e-07
(0.000113) 		2.79e-05
(0.0207) 		0.688
(1.00) 		0.109
(1.00) 		0.155
(1.00) 		0.00235
(1.00) 		0.174
(1.00) 		0.101
(1.00)
Del Peak 14(5q31 1) 277 (77%) 81 0.332
(1.00) 		0.228
(1.00) 		6.21e-07
(0.000477) 		3.25e-05
(0.0241) 		0.352
(1.00) 		0.209
(1.00) 		0.254
(1.00) 		0.401
(1.00) 		0.593
(1.00) 		0.00832
(1.00)
Del Peak 25(11p15 5) 173 (48%) 185 0.000689
(0.474) 		0.0528
(1.00) 		6.04e-05
(0.0445) 		0.0117
(1.00) 		0.000449
(0.314) 		2.34e-05
(0.0175) 		0.02
(1.00) 		0.0362
(1.00) 		0.0253
(1.00) 		0.0291
(1.00)
Del Peak 40(19q13 33) 96 (27%) 262 0.617
(1.00) 		0.0694
(1.00) 		4.76e-05
(0.0352) 		0.000249
(0.177) 		0.272
(1.00) 		0.635
(1.00) 		0.436
(1.00) 		0.212
(1.00) 		0.34
(1.00) 		0.119
(1.00)
Del Peak 47(Xp11 3) 116 (32%) 242 0.062
(1.00) 		0.175
(1.00) 		2.82e-06
(0.00215) 		5.16e-05
(0.038) 		0.0823
(1.00) 		0.0774
(1.00) 		0.0142
(1.00) 		0.0175
(1.00) 		0.133
(1.00) 		0.199
(1.00)
Amp Peak 1(1p34 2) 58 (16%) 300 0.028
(1.00) 		0.481
(1.00) 		0.000273
(0.193) 		0.71
(1.00) 		0.419
(1.00) 		0.668
(1.00) 		0.0484
(1.00) 		0.241
(1.00) 		0.299
(1.00) 		0.494
(1.00)
Amp Peak 2(1q21 2) 186 (52%) 172 0.0419
(1.00) 		0.00618
(1.00) 		7.32e-07
(0.000561) 		0.00128
(0.865) 		0.155
(1.00) 		0.0576
(1.00) 		0.000685
(0.472) 		0.000488
(0.34) 		0.305
(1.00) 		0.0562
(1.00)
Amp Peak 8(5p15 33) 281 (78%) 77 0.853
(1.00) 		0.867
(1.00) 		8.38e-06
(0.00632) 		0.0036
(1.00) 		0.498
(1.00) 		0.422
(1.00) 		0.387
(1.00) 		0.328
(1.00) 		0.841
(1.00) 		0.263
(1.00)
Amp Peak 9(5p12) 236 (66%) 122 0.919
(1.00) 		0.514
(1.00) 		1.38e-09
(1.08e-06) 		0.00666
(1.00) 		0.669
(1.00) 		1
(1.00) 		0.0635
(1.00) 		0.586
(1.00) 		0.0413
(1.00) 		0.219
(1.00)
Amp Peak 18(12p13 33) 177 (49%) 181 0.0102
(1.00) 		0.0571
(1.00) 		0.000255
(0.18) 		0.0112
(1.00) 		0.353
(1.00) 		0.711
(1.00) 		0.000575
(0.399) 		0.00518
(1.00) 		0.674
(1.00) 		0.429
(1.00)
Amp Peak 24(18p11 32) 122 (34%) 236 0.0602
(1.00) 		0.00628
(1.00) 		0.000148
(0.106) 		0.0328
(1.00) 		0.226
(1.00) 		0.844
(1.00) 		0.607
(1.00) 		0.177
(1.00) 		0.526
(1.00) 		0.163
(1.00)
Amp Peak 25(18q11 2) 115 (32%) 243 0.000456
(0.318) 		0.00227
(1.00) 		0.000231
(0.164) 		0.00415
(1.00) 		0.252
(1.00) 		0.771
(1.00) 		0.00438
(1.00) 		0.000578
(0.4) 		0.369
(1.00) 		0.00926
(1.00)
Amp Peak 26(19q12) 149 (42%) 209 0.455
(1.00) 		0.249
(1.00) 		0.000111
(0.0804) 		0.445
(1.00) 		0.274
(1.00) 		0.0244
(1.00) 		0.193
(1.00) 		0.082
(1.00) 		0.949
(1.00) 		0.686
(1.00)
Amp Peak 28(20p12 2) 193 (54%) 165 0.000987
(0.668) 		0.0043
(1.00) 		4.62e-08
(3.58e-05) 		0.00141
(0.949) 		0.95
(1.00) 		0.293
(1.00) 		0.15
(1.00) 		0.0134
(1.00) 		0.488
(1.00) 		0.246
(1.00)
Del Peak 4(2q22 1) 96 (27%) 262 0.255
(1.00) 		0.318
(1.00) 		0.000217
(0.155) 		0.0216
(1.00) 		0.653
(1.00) 		0.21
(1.00) 		0.188
(1.00) 		0.231
(1.00) 		0.683
(1.00) 		0.46
(1.00)
Del Peak 7(3p13) 310 (87%) 48 0.419
(1.00) 		0.549
(1.00) 		9.68e-05
(0.0703) 		0.00211
(1.00) 		0.91
(1.00) 		0.0127
(1.00) 		0.369
(1.00) 		0.0134
(1.00) 		0.872
(1.00) 		0.00826
(1.00)
Del Peak 9(4p15 31) 219 (61%) 139 0.000807
(0.551) 		0.00171
(1.00) 		1.21e-05
(0.00912) 		0.00406
(1.00) 		0.675
(1.00) 		0.0454
(1.00) 		0.0883
(1.00) 		0.0514
(1.00) 		0.403
(1.00) 		1
(1.00)
Del Peak 11(4q32 3) 226 (63%) 132 0.00967
(1.00) 		0.0253
(1.00) 		2.97e-07
(0.000229) 		0.0112
(1.00) 		0.102
(1.00) 		0.585
(1.00) 		0.0057
(1.00) 		0.036
(1.00) 		0.438
(1.00) 		0.144
(1.00)
Del Peak 12(4q35 2) 229 (64%) 129 0.1
(1.00) 		0.206
(1.00) 		1.07e-06
(0.00082) 		0.00259
(1.00) 		0.455
(1.00) 		0.561
(1.00) 		0.00532
(1.00) 		0.107
(1.00) 		0.671
(1.00) 		0.338
(1.00)
Del Peak 20(9p23) 234 (65%) 124 0.00561
(1.00) 		0.00291
(1.00) 		1.21e-07
(9.35e-05) 		0.109
(1.00) 		0.134
(1.00) 		0.185
(1.00) 		0.0261
(1.00) 		0.0876
(1.00) 		1
(1.00) 		0.0901
(1.00)
Del Peak 21(9p21 3) 272 (76%) 86 0.372
(1.00) 		0.172
(1.00) 		3.23e-06
(0.00246) 		0.517
(1.00) 		0.679
(1.00) 		0.379
(1.00) 		0.164
(1.00) 		0.846
(1.00) 		0.865
(1.00) 		0.337
(1.00)
Del Peak 39(19p13 3) 163 (46%) 195 0.334
(1.00) 		0.0231
(1.00) 		0.000227
(0.162) 		0.14
(1.00) 		0.0928
(1.00) 		0.404
(1.00) 		0.16
(1.00) 		0.0124
(1.00) 		0.0179
(1.00) 		0.0478
(1.00)
Del Peak 41(19q13 43) 96 (27%) 262 0.644
(1.00) 		0.207
(1.00) 		9.08e-05
(0.0661) 		0.000797
(0.546) 		0.466
(1.00) 		0.47
(1.00) 		0.465
(1.00) 		0.154
(1.00) 		0.216
(1.00) 		0.308
(1.00)
Del Peak 43(21q22 3) 205 (57%) 153 0.957
(1.00) 		0.193
(1.00) 		2.21e-08
(1.72e-05) 		0.00109
(0.737) 		0.478
(1.00) 		0.14
(1.00) 		0.564
(1.00) 		0.302
(1.00) 		0.00871
(1.00) 		0.474
(1.00)
Del Peak 45(Xp22 2) 114 (32%) 244 0.599
(1.00) 		0.351
(1.00) 		1.57e-05
(0.0118) 		0.0164
(1.00) 		0.343
(1.00) 		0.664
(1.00) 		0.14
(1.00) 		0.122
(1.00) 		0.195
(1.00) 		0.267
(1.00)
Del Peak 46(Xp21 1) 118 (33%) 240 0.354
(1.00) 		0.148
(1.00) 		2e-05
(0.015) 		0.00181
(1.00) 		0.381
(1.00) 		0.57
(1.00) 		0.0779
(1.00) 		0.00716
(1.00) 		0.407
(1.00) 		0.109
(1.00)
Del Peak 48(Xq22 3) 91 (25%) 267 0.00853
(1.00) 		0.105
(1.00) 		1.03e-05
(0.00777) 		0.000861
(0.586) 		0.745
(1.00) 		0.935
(1.00) 		0.0513
(1.00) 		0.485
(1.00) 		0.716
(1.00) 		0.954
(1.00)
Amp Peak 5(3p11 1) 73 (20%) 285 0.0748
(1.00) 		0.844
(1.00) 		0.673
(1.00) 		0.826
(1.00) 		0.202
(1.00) 		0.000831
(0.567) 		0.0555
(1.00) 		0.444
(1.00) 		0.41
(1.00) 		0.947
(1.00)
Amp Peak 7(4q12) 85 (24%) 273 0.679
(1.00) 		0.759
(1.00) 		0.00548
(1.00) 		0.284
(1.00) 		0.312
(1.00) 		0.0883
(1.00) 		0.555
(1.00) 		0.75
(1.00) 		0.185
(1.00) 		0.577
(1.00)
Amp Peak 10(6q12) 107 (30%) 251 1
(1.00) 		0.873
(1.00) 		0.069
(1.00) 		0.26
(1.00) 		0.349
(1.00) 		0.496
(1.00) 		0.395
(1.00) 		0.236
(1.00) 		0.595
(1.00) 		0.155
(1.00)
Amp Peak 11(7p11 2) 174 (49%) 184 0.186
(1.00) 		0.0939
(1.00) 		0.00168
(1.00) 		0.00254
(1.00) 		0.642
(1.00) 		0.85
(1.00) 		0.076
(1.00) 		0.0148
(1.00) 		0.7
(1.00) 		0.123
(1.00)
Amp Peak 13(8p11 23) 168 (47%) 190 0.00812
(1.00) 		0.168
(1.00) 		0.113
(1.00) 		0.1
(1.00) 		0.217
(1.00) 		0.0871
(1.00) 		0.00631
(1.00) 		0.72
(1.00) 		0.135
(1.00) 		0.62
(1.00)
Amp Peak 14(8q24 21) 248 (69%) 110 0.871
(1.00) 		0.644
(1.00) 		0.339
(1.00) 		0.589
(1.00) 		0.958
(1.00) 		0.768
(1.00) 		0.734
(1.00) 		0.428
(1.00) 		0.491
(1.00) 		0.932
(1.00)
Amp Peak 15(9p24 1) 67 (19%) 291 0.375
(1.00) 		0.0295
(1.00) 		0.000586
(0.405) 		0.228
(1.00) 		0.00176
(1.00) 		0.00573
(1.00) 		0.0413
(1.00) 		0.00294
(1.00) 		0.561
(1.00) 		0.39
(1.00)
Amp Peak 16(9p13 3) 98 (27%) 260 0.17
(1.00) 		0.373
(1.00) 		0.0107
(1.00) 		0.388
(1.00) 		0.0779
(1.00) 		0.00937
(1.00) 		0.022
(1.00) 		0.188
(1.00) 		0.408
(1.00) 		0.889
(1.00)
Amp Peak 17(11q13 3) 131 (37%) 227 0.0697
(1.00) 		0.0306
(1.00) 		0.0256
(1.00) 		0.00148
(0.992) 		0.184
(1.00) 		0.0641
(1.00) 		0.0125
(1.00) 		0.139
(1.00) 		0.15
(1.00) 		0.33
(1.00)
Amp Peak 19(12q15) 132 (37%) 226 0.312
(1.00) 		0.527
(1.00) 		0.00874
(1.00) 		0.0105
(1.00) 		0.806
(1.00) 		0.409
(1.00) 		0.105
(1.00) 		0.0491
(1.00) 		0.565
(1.00) 		0.926
(1.00)
Amp Peak 20(13q34) 64 (18%) 294 0.964
(1.00) 		0.0489
(1.00) 		0.396
(1.00) 		0.166
(1.00) 		0.824
(1.00) 		0.196
(1.00) 		0.803
(1.00) 		0.407
(1.00) 		0.0724
(1.00) 		0.251
(1.00)
Amp Peak 21(14q13 3) 110 (31%) 248 0.345
(1.00) 		0.246
(1.00) 		0.528
(1.00) 		0.47
(1.00) 		0.509
(1.00) 		0.0202
(1.00) 		0.617
(1.00) 		0.0847
(1.00) 		0.0167
(1.00) 		0.081
(1.00)
Amp Peak 27(19q13 2) 157 (44%) 201 0.473
(1.00) 		0.909
(1.00) 		0.000447
(0.313) 		0.25
(1.00) 		0.318
(1.00) 		0.131
(1.00) 		0.454
(1.00) 		0.0336
(1.00) 		0.975
(1.00) 		0.286
(1.00)
Amp Peak 29(20q11 21) 206 (58%) 152 0.991
(1.00) 		0.844
(1.00) 		0.00275
(1.00) 		0.0388
(1.00) 		0.743
(1.00) 		0.697
(1.00) 		0.593
(1.00) 		0.549
(1.00) 		0.937
(1.00) 		0.615
(1.00)
Amp Peak 30(22q11 21) 177 (49%) 181 0.111
(1.00) 		0.123
(1.00) 		0.0146
(1.00) 		0.00291
(1.00) 		0.874
(1.00) 		0.339
(1.00) 		0.0671
(1.00) 		0.0677
(1.00) 		0.816
(1.00) 		0.132
(1.00)
Amp Peak 31(Xq28) 92 (26%) 266 0.644
(1.00) 		0.515
(1.00) 		0.24
(1.00) 		0.0981
(1.00) 		0.0546
(1.00) 		0.0722
(1.00) 		0.143
(1.00) 		0.225
(1.00) 		0.754
(1.00) 		0.804
(1.00)
Del Peak 3(2p25 3) 34 (9%) 324 0.0461
(1.00) 		0.179
(1.00) 		0.0899
(1.00) 		0.367
(1.00) 		0.11
(1.00) 		0.789
(1.00) 		0.32
(1.00) 		0.226
(1.00) 		0.105
(1.00) 		0.0641
(1.00)
Del Peak 6(3p25 3) 285 (80%) 73 0.54
(1.00) 		0.176
(1.00) 		0.0292
(1.00) 		0.00407
(1.00) 		0.624
(1.00) 		0.212
(1.00) 		0.327
(1.00) 		0.00876
(1.00) 		0.655
(1.00) 		0.0137
(1.00)
Del Peak 10(4q22 1) 199 (56%) 159 0.00685
(1.00) 		0.0579
(1.00) 		0.000473
(0.33) 		0.0405
(1.00) 		0.147
(1.00) 		0.346
(1.00) 		0.0252
(1.00) 		0.00636
(1.00) 		0.37
(1.00) 		0.134
(1.00)
Del Peak 15(6p25 3) 90 (25%) 268 0.22
(1.00) 		0.11
(1.00) 		0.0169
(1.00) 		0.000692
(0.475) 		0.542
(1.00) 		0.00967
(1.00) 		0.01
(1.00) 		0.0204
(1.00) 		0.238
(1.00) 		0.179
(1.00)
Del Peak 16(6q26) 93 (26%) 265 0.0659
(1.00) 		0.00298
(1.00) 		0.00901
(1.00) 		0.00168
(1.00) 		0.885
(1.00) 		0.866
(1.00) 		0.0687
(1.00) 		0.141
(1.00) 		0.226
(1.00) 		0.108
(1.00)
Del Peak 17(7q11 22) 35 (10%) 323 0.908
(1.00) 		0.405
(1.00) 		0.000385
(0.271) 		0.394
(1.00) 		0.958
(1.00) 		0.8
(1.00) 		0.0463
(1.00) 		0.0644
(1.00) 		0.804
(1.00) 		0.526
(1.00)
Del Peak 18(7q36 1) 73 (20%) 285 0.393
(1.00) 		0.569
(1.00) 		0.0143
(1.00) 		0.381
(1.00) 		1
(1.00) 		0.286
(1.00) 		0.115
(1.00) 		0.388
(1.00) 		0.361
(1.00) 		0.828
(1.00)
Del Peak 19(8p23 2) 243 (68%) 115 0.864
(1.00) 		0.459
(1.00) 		0.00493
(1.00) 		0.295
(1.00) 		0.382
(1.00) 		0.196
(1.00) 		0.157
(1.00) 		0.072
(1.00) 		0.451
(1.00) 		0.167
(1.00)
Del Peak 23(10p15 3) 160 (45%) 198 0.373
(1.00) 		0.442
(1.00) 		0.0015
(1.00) 		0.000931
(0.633) 		0.407
(1.00) 		0.391
(1.00) 		0.00383
(1.00) 		0.0165
(1.00) 		0.104
(1.00) 		0.00185
(1.00)
Del Peak 26(11q22 1) 108 (30%) 250 0.493
(1.00) 		0.288
(1.00) 		0.00281
(1.00) 		0.0775
(1.00) 		0.0868
(1.00) 		0.975
(1.00) 		0.245
(1.00) 		0.423
(1.00) 		0.278
(1.00) 		0.0526
(1.00)
Del Peak 27(11q25) 131 (37%) 227 0.798
(1.00) 		0.429
(1.00) 		0.0229
(1.00) 		0.381
(1.00) 		0.109
(1.00) 		0.867
(1.00) 		0.447
(1.00) 		0.406
(1.00) 		0.185
(1.00) 		0.171
(1.00)
Del Peak 28(12q24 31) 57 (16%) 301 0.965
(1.00) 		0.332
(1.00) 		0.598
(1.00) 		0.303
(1.00) 		0.359
(1.00) 		0.203
(1.00) 		0.9
(1.00) 		0.689
(1.00) 		0.118
(1.00) 		0.302
(1.00)
Del Peak 29(13q12 11) 240 (67%) 118 0.0547
(1.00) 		0.611
(1.00) 		0.0338
(1.00) 		0.156
(1.00) 		1
(1.00) 		0.193
(1.00) 		0.7
(1.00) 		0.214
(1.00) 		0.958
(1.00) 		0.987
(1.00)
Del Peak 30(13q14 2) 251 (70%) 107 0.0512
(1.00) 		0.0962
(1.00) 		0.00073
(0.501) 		0.129
(1.00) 		0.85
(1.00) 		0.547
(1.00) 		0.0281
(1.00) 		0.147
(1.00) 		0.654
(1.00) 		0.543
(1.00)
Del Peak 31(14q11 2) 130 (36%) 228 0.0546
(1.00) 		0.293
(1.00) 		0.0383
(1.00) 		0.321
(1.00) 		0.243
(1.00) 		0.152
(1.00) 		0.00265
(1.00) 		0.00213
(1.00) 		0.333
(1.00) 		0.172
(1.00)
Del Peak 32(15q12) 122 (34%) 236 0.725
(1.00) 		0.228
(1.00) 		0.334
(1.00) 		0.317
(1.00) 		0.0697
(1.00) 		0.00674
(1.00) 		0.132
(1.00) 		0.356
(1.00) 		0.0996
(1.00) 		0.738
(1.00)
Del Peak 33(16p13 3) 129 (36%) 229 0.239
(1.00) 		0.245
(1.00) 		0.00318
(1.00) 		0.362
(1.00) 		0.135
(1.00) 		0.496
(1.00) 		0.531
(1.00) 		0.247
(1.00) 		0.643
(1.00) 		0.164
(1.00)
Del Peak 34(16q23 1) 144 (40%) 214 0.942
(1.00) 		0.659
(1.00) 		0.0506
(1.00) 		0.312
(1.00) 		0.336
(1.00) 		0.861
(1.00) 		0.205
(1.00) 		0.0264
(1.00) 		0.441
(1.00) 		0.581
(1.00)
Del Peak 35(17p11 2) 185 (52%) 173 0.194
(1.00) 		0.401
(1.00) 		0.004
(1.00) 		0.136
(1.00) 		0.135
(1.00) 		0.0101
(1.00) 		0.368
(1.00) 		0.86
(1.00) 		0.0697
(1.00) 		0.022
(1.00)
Del Peak 37(17q25 3) 68 (19%) 290 0.00493
(1.00) 		0.022
(1.00) 		0.000468
(0.327) 		0.0796
(1.00) 		0.782
(1.00) 		0.972
(1.00) 		0.0423
(1.00) 		0.000553
(0.384) 		0.581
(1.00) 		0.0108
(1.00)
Del Peak 38(18q23) 164 (46%) 194 0.508
(1.00) 		0.788
(1.00) 		0.517
(1.00) 		0.97
(1.00) 		0.858
(1.00) 		0.325
(1.00) 		0.23
(1.00) 		0.115
(1.00) 		0.804
(1.00) 		0.536
(1.00)
Del Peak 42(21q11 2) 176 (49%) 182 0.558
(1.00) 		0.223
(1.00) 		0.0058
(1.00) 		0.0647
(1.00) 		0.966
(1.00) 		0.904
(1.00) 		0.908
(1.00) 		0.485
(1.00) 		0.203
(1.00) 		0.233
(1.00)
Del Peak 44(22q11 21) 62 (17%) 296 0.0904
(1.00) 		0.0093
(1.00) 		0.172
(1.00) 		0.342
(1.00) 		0.125
(1.00) 		0.114
(1.00) 		0.598
(1.00) 		0.748
(1.00) 		0.149
(1.00) 		0.101
(1.00)
'Amp Peak 1(1p34.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000273 (Fisher's exact test), Q value = 0.19

Table S1.  Gene #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 1(1P34.2) MUTATED 17 9 32
AMP PEAK 1(1P34.2) WILD-TYPE 112 103 85

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 2(1q21.2) mutation analysis' versus 'CN_CNMF'

P value = 7.32e-07 (Fisher's exact test), Q value = 0.00056

Table S2.  Gene #2: 'Amp Peak 2(1q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 2(1Q21.2) MUTATED 52 81 53
AMP PEAK 2(1Q21.2) WILD-TYPE 77 31 64

Figure S2.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 3(2p16.1) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000305 (Fisher's exact test), Q value = 0.22

Table S3.  Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
AMP PEAK 3(2P16.1) MUTATED 19 40 12 15
AMP PEAK 3(2P16.1) WILD-TYPE 24 10 18 16

Figure S3.  Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 3(2p16.1) mutation analysis' versus 'CN_CNMF'

P value = 2.41e-09 (Fisher's exact test), Q value = 1.9e-06

Table S4.  Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 3(2P16.1) MUTATED 48 86 60
AMP PEAK 3(2P16.1) WILD-TYPE 81 26 57

Figure S4.  Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 3(2p16.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.051

Table S5.  Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
AMP PEAK 3(2P16.1) MUTATED 41 56 25
AMP PEAK 3(2P16.1) WILD-TYPE 49 19 34

Figure S5.  Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 3(2p16.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000333 (Fisher's exact test), Q value = 0.23

Table S6.  Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 80 79 38
AMP PEAK 3(2P16.1) MUTATED 23 58 44 17
AMP PEAK 3(2P16.1) WILD-TYPE 37 22 35 21

Figure S6.  Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 4(2q31.2) mutation analysis' versus 'CN_CNMF'

P value = 6.74e-05 (Fisher's exact test), Q value = 0.049

Table S7.  Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 4(2Q31.2) MUTATED 29 55 37
AMP PEAK 4(2Q31.2) WILD-TYPE 100 57 80

Figure S7.  Get High-res Image Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 4(2q31.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.94e-06 (Fisher's exact test), Q value = 0.0038

Table S8.  Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
AMP PEAK 4(2Q31.2) MUTATED 26 42 10
AMP PEAK 4(2Q31.2) WILD-TYPE 64 33 49

Figure S8.  Get High-res Image Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 6(3q26.33) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.013

Table S9.  Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
AMP PEAK 6(3Q26.33) MUTATED 19 54 67
AMP PEAK 6(3Q26.33) WILD-TYPE 9 0 5

Figure S9.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 6(3q26.33) mutation analysis' versus 'CN_CNMF'

P value = 1.63e-09 (Fisher's exact test), Q value = 1.3e-06

Table S10.  Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 6(3Q26.33) MUTATED 104 112 114
AMP PEAK 6(3Q26.33) WILD-TYPE 25 0 3

Figure S10.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 6(3q26.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.082

Table S11.  Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
AMP PEAK 6(3Q26.33) MUTATED 76 75 57
AMP PEAK 6(3Q26.33) WILD-TYPE 14 0 2

Figure S11.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 6(3q26.33) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.81e-05 (Fisher's exact test), Q value = 0.028

Table S12.  Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 80 79 38
AMP PEAK 6(3Q26.33) MUTATED 57 80 66 31
AMP PEAK 6(3Q26.33) WILD-TYPE 3 0 13 7

Figure S12.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 6(3q26.33) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000164 (Fisher's exact test), Q value = 0.12

Table S13.  Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
AMP PEAK 6(3Q26.33) MUTATED 100 86 48
AMP PEAK 6(3Q26.33) WILD-TYPE 16 0 7

Figure S13.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(3q26.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.11e-05 (Fisher's exact test), Q value = 0.066

Table S14.  Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 173 108
AMP PEAK 6(3Q26.33) MUTATED 50 150 106
AMP PEAK 6(3Q26.33) WILD-TYPE 0 23 2

Figure S14.  Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 8(5p15.33) mutation analysis' versus 'CN_CNMF'

P value = 8.38e-06 (Fisher's exact test), Q value = 0.0063

Table S15.  Gene #8: 'Amp Peak 8(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 8(5P15.33) MUTATED 89 84 108
AMP PEAK 8(5P15.33) WILD-TYPE 40 28 9

Figure S15.  Get High-res Image Gene #8: 'Amp Peak 8(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 9(5p12) mutation analysis' versus 'CN_CNMF'

P value = 1.38e-09 (Fisher's exact test), Q value = 1.1e-06

Table S16.  Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 9(5P12) MUTATED 63 72 101
AMP PEAK 9(5P12) WILD-TYPE 66 40 16

Figure S16.  Get High-res Image Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.36e-10 (Fisher's exact test), Q value = 2.6e-07

Table S17.  Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 12(7Q21.2) MUTATED 44 85 59
AMP PEAK 12(7Q21.2) WILD-TYPE 85 27 58

Figure S17.  Get High-res Image Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 8.35e-06 (Fisher's exact test), Q value = 0.0063

Table S18.  Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
AMP PEAK 12(7Q21.2) MUTATED 32 54 26
AMP PEAK 12(7Q21.2) WILD-TYPE 58 21 33

Figure S18.  Get High-res Image Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 18(12p13.33) mutation analysis' versus 'CN_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.18

Table S19.  Gene #18: 'Amp Peak 18(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 18(12P13.33) MUTATED 48 71 58
AMP PEAK 18(12P13.33) WILD-TYPE 81 41 59

Figure S19.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'CN_CNMF'

P value = 5.63e-07 (Fisher's exact test), Q value = 0.00043

Table S20.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 22(15Q26.3) MUTATED 25 58 45
AMP PEAK 22(15Q26.3) WILD-TYPE 104 54 72

Figure S20.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.78e-05 (Fisher's exact test), Q value = 0.013

Table S21.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
AMP PEAK 22(15Q26.3) MUTATED 15 37 24
AMP PEAK 22(15Q26.3) WILD-TYPE 75 38 35

Figure S21.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.14e-05 (Fisher's exact test), Q value = 0.052

Table S22.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 173 108
AMP PEAK 22(15Q26.3) MUTATED 28 46 49
AMP PEAK 22(15Q26.3) WILD-TYPE 22 127 59

Figure S22.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(17q25.1) mutation analysis' versus 'CN_CNMF'

P value = 1.87e-06 (Fisher's exact test), Q value = 0.0014

Table S23.  Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 23(17Q25.1) MUTATED 40 71 60
AMP PEAK 23(17Q25.1) WILD-TYPE 89 41 57

Figure S23.  Get High-res Image Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 23(17q25.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.11

Table S24.  Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
AMP PEAK 23(17Q25.1) MUTATED 35 49 19
AMP PEAK 23(17Q25.1) WILD-TYPE 55 26 40

Figure S24.  Get High-res Image Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 24(18p11.32) mutation analysis' versus 'CN_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.11

Table S25.  Gene #24: 'Amp Peak 24(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 24(18P11.32) MUTATED 29 54 39
AMP PEAK 24(18P11.32) WILD-TYPE 100 58 78

Figure S25.  Get High-res Image Gene #24: 'Amp Peak 24(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 25(18q11.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000231 (Fisher's exact test), Q value = 0.16

Table S26.  Gene #25: 'Amp Peak 25(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 25(18Q11.2) MUTATED 26 50 39
AMP PEAK 25(18Q11.2) WILD-TYPE 103 62 78

Figure S26.  Get High-res Image Gene #25: 'Amp Peak 25(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'CN_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.08

Table S27.  Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 26(19Q12) MUTATED 42 65 42
AMP PEAK 26(19Q12) WILD-TYPE 87 47 75

Figure S27.  Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 28(20p12.2) mutation analysis' versus 'CN_CNMF'

P value = 4.62e-08 (Fisher's exact test), Q value = 3.6e-05

Table S28.  Gene #28: 'Amp Peak 28(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
AMP PEAK 28(20P12.2) MUTATED 48 83 62
AMP PEAK 28(20P12.2) WILD-TYPE 81 29 55

Figure S28.  Get High-res Image Gene #28: 'Amp Peak 28(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.28e-06 (Fisher's exact test), Q value = 0.00098

Table S29.  Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 1(1P36.32) MUTATED 9 37 12 10
DEL PEAK 1(1P36.32) WILD-TYPE 34 13 18 21

Figure S29.  Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 1.29e-08 (Fisher's exact test), Q value = 1e-05

Table S30.  Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 1(1P36.32) MUTATED 10 41 17
DEL PEAK 1(1P36.32) WILD-TYPE 18 13 55

Figure S30.  Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 3.34e-28 (Fisher's exact test), Q value = 2.6e-25

Table S31.  Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 1(1P36.32) MUTATED 33 96 26
DEL PEAK 1(1P36.32) WILD-TYPE 96 16 91

Figure S31.  Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 4.78e-16 (Fisher's exact test), Q value = 3.8e-13

Table S32.  Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
DEL PEAK 1(1P36.32) MUTATED 15 59 19
DEL PEAK 1(1P36.32) WILD-TYPE 75 16 40

Figure S32.  Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.02e-10 (Fisher's exact test), Q value = 8e-08

Table S33.  Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 80 79 38
DEL PEAK 1(1P36.32) MUTATED 16 61 26 11
DEL PEAK 1(1P36.32) WILD-TYPE 44 19 53 27

Figure S33.  Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 6.75e-09 (Fisher's exact test), Q value = 5.3e-06

Table S34.  Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
DEL PEAK 1(1P36.32) MUTATED 37 61 16
DEL PEAK 1(1P36.32) WILD-TYPE 79 25 39

Figure S34.  Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p13.2) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.17

Table S35.  Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 2(1P13.2) MUTATED 17 35 8 10
DEL PEAK 2(1P13.2) WILD-TYPE 26 15 22 21

Figure S35.  Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 6.47e-14 (Fisher's exact test), Q value = 5.1e-11

Table S36.  Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 2(1P13.2) MUTATED 34 82 40
DEL PEAK 2(1P13.2) WILD-TYPE 95 30 77

Figure S36.  Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 6.52e-09 (Fisher's exact test), Q value = 5.1e-06

Table S37.  Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
DEL PEAK 2(1P13.2) MUTATED 19 51 24
DEL PEAK 2(1P13.2) WILD-TYPE 71 24 35

Figure S37.  Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 2.35e-05 (Fisher's exact test), Q value = 0.018

Table S38.  Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 80 79 38
DEL PEAK 2(1P13.2) MUTATED 23 53 25 12
DEL PEAK 2(1P13.2) WILD-TYPE 37 27 54 26

Figure S38.  Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 7.07e-05 (Fisher's exact test), Q value = 0.052

Table S39.  Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
DEL PEAK 2(1P13.2) MUTATED 38 54 21
DEL PEAK 2(1P13.2) WILD-TYPE 78 32 34

Figure S39.  Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000217 (Fisher's exact test), Q value = 0.15

Table S40.  Gene #35: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 4(2Q22.1) MUTATED 19 41 36
DEL PEAK 4(2Q22.1) WILD-TYPE 110 71 81

Figure S40.  Get High-res Image Gene #35: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 5(2q36.2) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.17

Table S41.  Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 5(2Q36.2) MUTATED 9 26 3 12
DEL PEAK 5(2Q36.2) WILD-TYPE 34 24 27 19

Figure S41.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 5(2q36.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.035

Table S42.  Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 5(2Q36.2) MUTATED 5 30 15
DEL PEAK 5(2Q36.2) WILD-TYPE 23 24 57

Figure S42.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(2q36.2) mutation analysis' versus 'CN_CNMF'

P value = 5.32e-12 (Fisher's exact test), Q value = 4.2e-09

Table S43.  Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 5(2Q36.2) MUTATED 20 65 31
DEL PEAK 5(2Q36.2) WILD-TYPE 109 47 86

Figure S43.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 5(2q36.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.25

Table S44.  Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
DEL PEAK 5(2Q36.2) MUTATED 19 38 19
DEL PEAK 5(2Q36.2) WILD-TYPE 71 37 40

Figure S44.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 5(2q36.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.49e-05 (Fisher's exact test), Q value = 0.062

Table S45.  Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 80 79 38
DEL PEAK 5(2Q36.2) MUTATED 17 40 18 5
DEL PEAK 5(2Q36.2) WILD-TYPE 43 40 61 33

Figure S45.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 5(2q36.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.15e-06 (Fisher's exact test), Q value = 0.0047

Table S46.  Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
DEL PEAK 5(2Q36.2) MUTATED 23 44 13
DEL PEAK 5(2Q36.2) WILD-TYPE 93 42 42

Figure S46.  Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 9.68e-05 (Fisher's exact test), Q value = 0.07

Table S47.  Gene #38: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 7(3P13) MUTATED 98 104 108
DEL PEAK 7(3P13) WILD-TYPE 31 8 9

Figure S47.  Get High-res Image Gene #38: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 8(3p12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.46e-07 (Fisher's exact test), Q value = 0.00011

Table S48.  Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 8(3P12.1) MUTATED 80 101 99
DEL PEAK 8(3P12.1) WILD-TYPE 49 11 18

Figure S48.  Get High-res Image Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 8(3p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.021

Table S49.  Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
DEL PEAK 8(3P12.1) MUTATED 59 66 55
DEL PEAK 8(3P12.1) WILD-TYPE 31 9 4

Figure S49.  Get High-res Image Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 9(4p15.31) mutation analysis' versus 'CN_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0091

Table S50.  Gene #40: 'Del Peak 9(4p15.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 9(4P15.31) MUTATED 65 88 66
DEL PEAK 9(4P15.31) WILD-TYPE 64 24 51

Figure S50.  Get High-res Image Gene #40: 'Del Peak 9(4p15.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 11(4q32.3) mutation analysis' versus 'CN_CNMF'

P value = 2.97e-07 (Fisher's exact test), Q value = 0.00023

Table S51.  Gene #42: 'Del Peak 11(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 11(4Q32.3) MUTATED 67 93 66
DEL PEAK 11(4Q32.3) WILD-TYPE 62 19 51

Figure S51.  Get High-res Image Gene #42: 'Del Peak 11(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(4q35.2) mutation analysis' versus 'CN_CNMF'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00082

Table S52.  Gene #43: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 12(4Q35.2) MUTATED 70 93 66
DEL PEAK 12(4Q35.2) WILD-TYPE 59 19 51

Figure S52.  Get High-res Image Gene #43: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 5.71e-10 (Fisher's exact test), Q value = 4.5e-07

Table S53.  Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 13(5Q11.2) MUTATED 69 96 100
DEL PEAK 13(5Q11.2) WILD-TYPE 60 16 17

Figure S53.  Get High-res Image Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(5q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000266 (Fisher's exact test), Q value = 0.19

Table S54.  Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
DEL PEAK 13(5Q11.2) MUTATED 54 62 51
DEL PEAK 13(5Q11.2) WILD-TYPE 36 13 8

Figure S54.  Get High-res Image Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 13(5q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000162 (Fisher's exact test), Q value = 0.12

Table S55.  Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 173 108
DEL PEAK 13(5Q11.2) MUTATED 39 115 95
DEL PEAK 13(5Q11.2) WILD-TYPE 11 58 13

Figure S55.  Get High-res Image Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(5q31.1) mutation analysis' versus 'CN_CNMF'

P value = 6.21e-07 (Fisher's exact test), Q value = 0.00048

Table S56.  Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 14(5Q31.1) MUTATED 79 97 101
DEL PEAK 14(5Q31.1) WILD-TYPE 50 15 16

Figure S56.  Get High-res Image Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 14(5q31.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.25e-05 (Fisher's exact test), Q value = 0.024

Table S57.  Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
DEL PEAK 14(5Q31.1) MUTATED 58 64 55
DEL PEAK 14(5Q31.1) WILD-TYPE 32 11 4

Figure S57.  Get High-res Image Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 20(9p23) mutation analysis' versus 'CN_CNMF'

P value = 1.21e-07 (Fisher's exact test), Q value = 9.4e-05

Table S58.  Gene #51: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 20(9P23) MUTATED 68 67 99
DEL PEAK 20(9P23) WILD-TYPE 61 45 18

Figure S58.  Get High-res Image Gene #51: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 21(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 3.23e-06 (Fisher's exact test), Q value = 0.0025

Table S59.  Gene #52: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 21(9P21.3) MUTATED 81 86 105
DEL PEAK 21(9P21.3) WILD-TYPE 48 26 12

Figure S59.  Get High-res Image Gene #52: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 22(9q21.11) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.13

Table S60.  Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 22(9Q21.11) MUTATED 28 12 19 15
DEL PEAK 22(9Q21.11) WILD-TYPE 15 38 11 16

Figure S60.  Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 22(9q21.11) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.92e-05 (Fisher's exact test), Q value = 0.036

Table S61.  Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 22(9Q21.11) MUTATED 16 13 45
DEL PEAK 22(9Q21.11) WILD-TYPE 12 41 27

Figure S61.  Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 22(9q21.11) mutation analysis' versus 'CN_CNMF'

P value = 2.03e-07 (Fisher's exact test), Q value = 0.00016

Table S62.  Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 22(9Q21.11) MUTATED 62 34 78
DEL PEAK 22(9Q21.11) WILD-TYPE 67 78 39

Figure S62.  Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 22(9q21.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.42e-06 (Fisher's exact test), Q value = 0.0011

Table S63.  Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
DEL PEAK 22(9Q21.11) MUTATED 49 19 40
DEL PEAK 22(9Q21.11) WILD-TYPE 41 56 19

Figure S63.  Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 22(9q21.11) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.44e-06 (Fisher's exact test), Q value = 0.0034

Table S64.  Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 80 79 38
DEL PEAK 22(9Q21.11) MUTATED 33 19 48 22
DEL PEAK 22(9Q21.11) WILD-TYPE 27 61 31 16

Figure S64.  Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 22(9q21.11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.4e-07 (Fisher's exact test), Q value = 0.00018

Table S65.  Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
DEL PEAK 22(9Q21.11) MUTATED 64 21 37
DEL PEAK 22(9Q21.11) WILD-TYPE 52 65 18

Figure S65.  Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 22(9q21.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.16e-05 (Fisher's exact test), Q value = 0.023

Table S66.  Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 173 108
DEL PEAK 22(9Q21.11) MUTATED 10 90 61
DEL PEAK 22(9Q21.11) WILD-TYPE 40 83 47

Figure S66.  Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 24(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.14

Table S67.  Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 24(10Q23.31) MUTATED 53 75 56
DEL PEAK 24(10Q23.31) WILD-TYPE 76 37 61

Figure S67.  Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 24(10q23.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.42e-05 (Fisher's exact test), Q value = 0.047

Table S68.  Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
DEL PEAK 24(10Q23.31) MUTATED 33 53 30
DEL PEAK 24(10Q23.31) WILD-TYPE 57 22 29

Figure S68.  Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 24(10q23.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.075

Table S69.  Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 80 79 38
DEL PEAK 24(10Q23.31) MUTATED 22 57 35 16
DEL PEAK 24(10Q23.31) WILD-TYPE 38 23 44 22

Figure S69.  Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 24(10q23.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.02

Table S70.  Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
DEL PEAK 24(10Q23.31) MUTATED 42 59 29
DEL PEAK 24(10Q23.31) WILD-TYPE 74 27 26

Figure S70.  Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 6.04e-05 (Fisher's exact test), Q value = 0.044

Table S71.  Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 25(11P15.5) MUTATED 47 51 75
DEL PEAK 25(11P15.5) WILD-TYPE 82 61 42

Figure S71.  Get High-res Image Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 25(11p15.5) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.34e-05 (Fisher's exact test), Q value = 0.017

Table S72.  Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 48 58 41
DEL PEAK 25(11P15.5) MUTATED 35 17 29 11
DEL PEAK 25(11P15.5) WILD-TYPE 12 31 29 30

Figure S72.  Get High-res Image Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 36(17q11.2) mutation analysis' versus 'MRNA_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0095

Table S73.  Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 36(17Q11.2) MUTATED 21 3 11 7
DEL PEAK 36(17Q11.2) WILD-TYPE 22 47 19 24

Figure S73.  Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 36(17q11.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.44e-05 (Fisher's exact test), Q value = 0.047

Table S74.  Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 36(17Q11.2) MUTATED 9 4 29
DEL PEAK 36(17Q11.2) WILD-TYPE 19 50 43

Figure S74.  Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(17q11.2) mutation analysis' versus 'CN_CNMF'

P value = 9.35e-09 (Fisher's exact test), Q value = 7.3e-06

Table S75.  Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 36(17Q11.2) MUTATED 34 8 47
DEL PEAK 36(17Q11.2) WILD-TYPE 95 104 70

Figure S75.  Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 36(17q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.088

Table S76.  Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 80 79 38
DEL PEAK 36(17Q11.2) MUTATED 20 6 23 13
DEL PEAK 36(17Q11.2) WILD-TYPE 40 74 56 25

Figure S76.  Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 36(17q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.16e-06 (Fisher's exact test), Q value = 0.0054

Table S77.  Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
DEL PEAK 36(17Q11.2) MUTATED 39 6 17
DEL PEAK 36(17Q11.2) WILD-TYPE 77 80 38

Figure S77.  Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000227 (Fisher's exact test), Q value = 0.16

Table S78.  Gene #70: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 39(19P13.3) MUTATED 46 46 71
DEL PEAK 39(19P13.3) WILD-TYPE 83 66 46

Figure S78.  Get High-res Image Gene #70: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 40(19q13.33) mutation analysis' versus 'CN_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.035

Table S79.  Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 40(19Q13.33) MUTATED 20 46 30
DEL PEAK 40(19Q13.33) WILD-TYPE 109 66 87

Figure S79.  Get High-res Image Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 40(19q13.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.18

Table S80.  Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
DEL PEAK 40(19Q13.33) MUTATED 11 27 21
DEL PEAK 40(19Q13.33) WILD-TYPE 79 48 38

Figure S80.  Get High-res Image Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 41(19q13.43) mutation analysis' versus 'CN_CNMF'

P value = 9.08e-05 (Fisher's exact test), Q value = 0.066

Table S81.  Gene #72: 'Del Peak 41(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 41(19Q13.43) MUTATED 20 45 31
DEL PEAK 41(19Q13.43) WILD-TYPE 109 67 86

Figure S81.  Get High-res Image Gene #72: 'Del Peak 41(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 43(21q22.3) mutation analysis' versus 'CN_CNMF'

P value = 2.21e-08 (Fisher's exact test), Q value = 1.7e-05

Table S82.  Gene #74: 'Del Peak 43(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 43(21Q22.3) MUTATED 48 82 75
DEL PEAK 43(21Q22.3) WILD-TYPE 81 30 42

Figure S82.  Get High-res Image Gene #74: 'Del Peak 43(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 45(Xp22.2) mutation analysis' versus 'CN_CNMF'

P value = 1.57e-05 (Fisher's exact test), Q value = 0.012

Table S83.  Gene #76: 'Del Peak 45(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 45(XP22.2) MUTATED 22 48 44
DEL PEAK 45(XP22.2) WILD-TYPE 107 64 73

Figure S83.  Get High-res Image Gene #76: 'Del Peak 45(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 46(Xp21.1) mutation analysis' versus 'CN_CNMF'

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

Table S84.  Gene #77: 'Del Peak 46(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 46(XP21.1) MUTATED 24 51 43
DEL PEAK 46(XP21.1) WILD-TYPE 105 61 74

Figure S84.  Get High-res Image Gene #77: 'Del Peak 46(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 47(Xp11.3) mutation analysis' versus 'CN_CNMF'

P value = 2.82e-06 (Fisher's exact test), Q value = 0.0021

Table S85.  Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 47(XP11.3) MUTATED 22 52 42
DEL PEAK 47(XP11.3) WILD-TYPE 107 60 75

Figure S85.  Get High-res Image Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 47(Xp11.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.16e-05 (Fisher's exact test), Q value = 0.038

Table S86.  Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 75 59
DEL PEAK 47(XP11.3) MUTATED 15 36 22
DEL PEAK 47(XP11.3) WILD-TYPE 75 39 37

Figure S86.  Get High-res Image Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 48(Xq22.3) mutation analysis' versus 'CN_CNMF'

P value = 1.03e-05 (Fisher's exact test), Q value = 0.0078

Table S87.  Gene #79: 'Del Peak 48(Xq22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 112 117
DEL PEAK 48(XQ22.3) MUTATED 16 30 45
DEL PEAK 48(XQ22.3) WILD-TYPE 113 82 72

Figure S87.  Get High-res Image Gene #79: 'Del Peak 48(Xq22.3) mutation analysis' versus Clinical Feature #3: 'CN_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 = 358

  • Number of copy number variation regions = 79

  • Number of molecular subtypes = 10

  • 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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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