Lung Squamous Cell Carcinoma: Correlation between copy number variation genes and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 84 peak regions and 10 molecular subtypes across 397 patients, 99 significant findings detected with Q value < 0.25.

  • 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 13(7q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 19(12p13.33) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 23(15q26.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 24(17q25.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 25(18p11.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 26(18q11.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 28(19q13.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 29(20p12.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 31(22q11.21) cnvs correlated to 'CN_CNMF'.

  • Del Peak 1(1p36.22) 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(3p12.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 10(4p15.2) cnvs correlated to 'CN_CNMF'.

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

  • Del Peak 12(4q32.3) cnvs correlated to 'CN_CNMF'.

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

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

  • Del Peak 15(5q31.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 19(7q11.22) cnvs correlated to 'CN_CNMF'.

  • Del Peak 22(9p23) cnvs correlated to 'CN_CNMF'.

  • Del Peak 23(9p21.3) cnvs correlated to 'CN_CNMF'.

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

  • Del Peak 25(10p15.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

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

  • Del Peak 43(19p13.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 44(19q13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 84 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 99 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 24(9q21 11) 191 (48%) 206 0.000177
(0.134) 		4.92e-05
(0.0382) 		5.97e-11
(4.97e-08) 		1.14e-06
(0.000931) 		0.653
(1.00) 		0.239
(1.00) 		4.44e-06
(0.00357) 		2.4e-07
(0.000196) 		0.0643
(1.00) 		0.000283
(0.211)
Amp Peak 6(3q26 33) 364 (92%) 33 0.000427
(0.314) 		1.71e-05
(0.0135) 		7.05e-12
(5.88e-09) 		6.69e-07
(0.000545) 		0.193
(1.00) 		0.0776
(1.00) 		3.81e-05
(0.0297) 		0.000164
(0.125) 		0.238
(1.00) 		1.37e-05
(0.0109)
Del Peak 1(1p36 22) 172 (43%) 225 1.43e-06
(0.00116) 		1.78e-08
(1.47e-05) 		1.61e-28
(1.36e-25) 		2.1e-14
(1.76e-11) 		0.412
(1.00) 		0.0262
(1.00) 		1.09e-09
(9.05e-07) 		1.35e-08
(1.12e-05) 		0.0227
(1.00) 		0.00387
(1.00)
Del Peak 5(2q36 2) 132 (33%) 265 0.000236
(0.178) 		4.76e-05
(0.037) 		1.7e-12
(1.42e-09) 		2.14e-06
(0.00174) 		0.177
(1.00) 		0.126
(1.00) 		8.49e-05
(0.0653) 		6.15e-06
(0.00494) 		0.986
(1.00) 		0.587
(1.00)
Del Peak 2(1p13 2) 172 (43%) 225 0.000237
(0.178) 		0.00055
(0.4) 		1.23e-15
(1.03e-12) 		5.74e-09
(4.75e-06) 		0.119
(1.00) 		0.0712
(1.00) 		2.35e-05
(0.0185) 		7.07e-05
(0.0545) 		0.165
(1.00) 		0.0246
(1.00)
Del Peak 40(17q11 2) 96 (24%) 301 1.26e-05
(0.01) 		6.44e-05
(0.0497) 		3.04e-08
(2.51e-05) 		0.0177
(1.00) 		0.495
(1.00) 		0.378
(1.00) 		0.000122
(0.0932) 		7.16e-06
(0.00574) 		0.426
(1.00) 		0.0683
(1.00)
Amp Peak 3(2p16 1) 216 (54%) 181 0.000305
(0.227) 		0.00165
(1.00) 		3.18e-13
(2.66e-10) 		5.83e-05
(0.045) 		0.95
(1.00) 		0.643
(1.00) 		0.000333
(0.247) 		0.00113
(0.799) 		0.79
(1.00) 		0.043
(1.00)
Del Peak 27(10q23 31) 203 (51%) 194 0.0392
(1.00) 		0.00386
(1.00) 		2.17e-05
(0.017) 		2.08e-06
(0.00169) 		0.36
(1.00) 		0.39
(1.00) 		0.000104
(0.0793) 		2.63e-05
(0.0206) 		0.541
(1.00) 		0.0173
(1.00)
Del Peak 14(5q11 2) 290 (73%) 107 0.842
(1.00) 		0.303
(1.00) 		2.03e-12
(1.7e-09) 		0.000192
(0.145) 		0.959
(1.00) 		0.244
(1.00) 		0.248
(1.00) 		0.56
(1.00) 		0.953
(1.00) 		8.06e-05
(0.0621)
Del Peak 26(10p15 1) 168 (42%) 229 0.0722
(1.00) 		0.484
(1.00) 		0.000162
(0.123) 		4.03e-06
(0.00325) 		0.469
(1.00) 		0.353
(1.00) 		0.000259
(0.194) 		0.0131
(1.00) 		0.0442
(1.00) 		0.00516
(1.00)
Amp Peak 4(2q31 2) 132 (33%) 265 0.0207
(1.00) 		0.000948
(0.675) 		6.52e-06
(0.00523) 		1.99e-07
(0.000163) 		0.724
(1.00) 		0.887
(1.00) 		0.000801
(0.575) 		0.000932
(0.665) 		0.426
(1.00) 		0.37
(1.00)
Amp Peak 13(7q21 2) 209 (53%) 188 0.101
(1.00) 		0.25
(1.00) 		5.34e-10
(4.44e-07) 		1.27e-05
(0.0101) 		0.0573
(1.00) 		0.389
(1.00) 		0.0165
(1.00) 		0.0221
(1.00) 		0.122
(1.00) 		0.0892
(1.00)
Amp Peak 23(15q26 3) 139 (35%) 258 0.151
(1.00) 		0.021
(1.00) 		1.56e-05
(0.0123) 		9.39e-06
(0.0075) 		0.354
(1.00) 		0.0183
(1.00) 		0.000622
(0.45) 		0.00426
(1.00) 		0.0241
(1.00) 		0.000437
(0.321)
Amp Peak 24(17q25 1) 191 (48%) 206 0.0177
(1.00) 		0.0608
(1.00) 		6.01e-07
(0.00049) 		2.17e-05
(0.017) 		0.267
(1.00) 		0.292
(1.00) 		0.0274
(1.00) 		0.00807
(1.00) 		0.611
(1.00) 		0.893
(1.00)
Amp Peak 25(18p11 32) 137 (35%) 260 0.0958
(1.00) 		0.00981
(1.00) 		2.48e-05
(0.0195) 		0.000126
(0.096) 		0.231
(1.00) 		0.451
(1.00) 		0.41
(1.00) 		0.121
(1.00) 		0.66
(1.00) 		0.135
(1.00)
Amp Peak 29(20p12 2) 211 (53%) 186 0.000987
(0.698) 		0.0043
(1.00) 		8.92e-08
(7.34e-05) 		0.000161
(0.123) 		0.967
(1.00) 		0.221
(1.00) 		0.15
(1.00) 		0.0134
(1.00) 		0.611
(1.00) 		0.279
(1.00)
Del Peak 13(4q35 2) 253 (64%) 144 0.1
(1.00) 		0.206
(1.00) 		2.84e-06
(0.0023) 		0.000124
(0.0944) 		0.455
(1.00) 		0.47
(1.00) 		0.00532
(1.00) 		0.107
(1.00) 		0.63
(1.00) 		0.309
(1.00)
Del Peak 15(5q31 1) 308 (78%) 89 0.332
(1.00) 		0.228
(1.00) 		5.7e-09
(4.72e-06) 		3e-05
(0.0235) 		0.272
(1.00) 		0.166
(1.00) 		0.294
(1.00) 		0.445
(1.00) 		0.709
(1.00) 		0.000462
(0.339)
Del Peak 25(10p15 3) 178 (45%) 219 0.373
(1.00) 		0.442
(1.00) 		4.8e-05
(0.0373) 		9.6e-05
(0.0736) 		0.329
(1.00) 		0.443
(1.00) 		0.00383
(1.00) 		0.0165
(1.00) 		0.122
(1.00) 		0.00273
(1.00)
Del Peak 28(11p15 5) 183 (46%) 214 0.000689
(0.497) 		0.0528
(1.00) 		1.28e-06
(0.00104) 		0.0352
(1.00) 		0.000764
(0.549) 		2.02e-05
(0.0159) 		0.02
(1.00) 		0.0362
(1.00) 		0.0436
(1.00) 		0.0754
(1.00)
Del Peak 44(19q13 33) 106 (27%) 291 0.617
(1.00) 		0.0694
(1.00) 		0.000167
(0.126) 		0.000187
(0.141) 		0.244
(1.00) 		0.719
(1.00) 		0.436
(1.00) 		0.212
(1.00) 		0.438
(1.00) 		0.126
(1.00)
Del Peak 48(22q13 32) 95 (24%) 302 0.000281
(0.21) 		8.68e-05
(0.0667) 		0.0172
(1.00) 		0.351
(1.00) 		0.543
(1.00) 		0.0759
(1.00) 		0.0575
(1.00) 		0.162
(1.00) 		0.0961
(1.00) 		0.0162
(1.00)
Del Peak 50(Xp21 1) 127 (32%) 270 0.354
(1.00) 		0.148
(1.00) 		5.39e-05
(0.0417) 		0.00024
(0.18) 		0.344
(1.00) 		0.681
(1.00) 		0.0779
(1.00) 		0.00716
(1.00) 		0.321
(1.00) 		0.0974
(1.00)
Del Peak 51(Xp11 3) 125 (31%) 272 0.062
(1.00) 		0.175
(1.00) 		9.19e-06
(0.00735) 		4.09e-05
(0.0319) 		0.0923
(1.00) 		0.124
(1.00) 		0.0142
(1.00) 		0.0175
(1.00) 		0.0635
(1.00) 		0.193
(1.00)
Del Peak 52(Xq22 3) 95 (24%) 302 0.00853
(1.00) 		0.105
(1.00) 		1.91e-05
(0.015) 		0.000249
(0.187) 		0.663
(1.00) 		0.92
(1.00) 		0.0513
(1.00) 		0.485
(1.00) 		0.535
(1.00) 		0.942
(1.00)
Amp Peak 2(1q21 2) 205 (52%) 192 0.0419
(1.00) 		0.00618
(1.00) 		1.98e-07
(0.000163) 		0.00113
(0.798) 		0.16
(1.00) 		0.0492
(1.00) 		0.000685
(0.495) 		0.000488
(0.357) 		0.178
(1.00) 		0.0377
(1.00)
Amp Peak 8(5p15 33) 314 (79%) 83 0.853
(1.00) 		0.867
(1.00) 		1.07e-05
(0.00852) 		0.0129
(1.00) 		0.405
(1.00) 		0.502
(1.00) 		0.387
(1.00) 		0.328
(1.00) 		0.71
(1.00) 		0.18
(1.00)
Amp Peak 9(5p12) 261 (66%) 136 0.919
(1.00) 		0.514
(1.00) 		7.58e-10
(6.29e-07) 		0.00874
(1.00) 		0.563
(1.00) 		1
(1.00) 		0.0635
(1.00) 		0.586
(1.00) 		0.0397
(1.00) 		0.116
(1.00)
Amp Peak 19(12p13 33) 198 (50%) 199 0.0102
(1.00) 		0.0571
(1.00) 		1.23e-05
(0.00977) 		0.000492
(0.359) 		0.313
(1.00) 		0.729
(1.00) 		0.000575
(0.418) 		0.00518
(1.00) 		0.583
(1.00) 		0.539
(1.00)
Amp Peak 26(18q11 2) 126 (32%) 271 0.000456
(0.334) 		0.00227
(1.00) 		1.37e-05
(0.0108) 		0.000342
(0.253) 		0.272
(1.00) 		0.74
(1.00) 		0.00438
(1.00) 		0.000578
(0.419) 		0.32
(1.00) 		0.012
(1.00)
Amp Peak 27(19q12) 167 (42%) 230 0.455
(1.00) 		0.249
(1.00) 		4.07e-06
(0.00328) 		0.182
(1.00) 		0.231
(1.00) 		0.0287
(1.00) 		0.193
(1.00) 		0.082
(1.00) 		0.951
(1.00) 		0.609
(1.00)
Amp Peak 28(19q13 2) 170 (43%) 227 0.715
(1.00) 		1
(1.00) 		0.000195
(0.147) 		0.0708
(1.00) 		0.356
(1.00) 		0.117
(1.00) 		0.626
(1.00) 		0.053
(1.00) 		0.872
(1.00) 		0.454
(1.00)
Amp Peak 31(22q11 21) 199 (50%) 198 0.111
(1.00) 		0.123
(1.00) 		0.000296
(0.22) 		0.000477
(0.349) 		0.888
(1.00) 		0.349
(1.00) 		0.0671
(1.00) 		0.0677
(1.00) 		0.727
(1.00) 		0.103
(1.00)
Del Peak 4(2q22 1) 105 (26%) 292 0.255
(1.00) 		0.318
(1.00) 		0.000271
(0.203) 		0.0198
(1.00) 		0.667
(1.00) 		0.0777
(1.00) 		0.188
(1.00) 		0.231
(1.00) 		0.648
(1.00) 		0.551
(1.00)
Del Peak 7(3p13) 340 (86%) 57 0.419
(1.00) 		0.549
(1.00) 		2.67e-06
(0.00216) 		0.000858
(0.613) 		0.882
(1.00) 		0.0379
(1.00) 		0.369
(1.00) 		0.0134
(1.00) 		0.926
(1.00) 		0.0046
(1.00)
Del Peak 8(3p12 3) 332 (84%) 65 0.258
(1.00) 		0.342
(1.00) 		3.03e-05
(0.0236) 		0.00259
(1.00) 		1
(1.00) 		0.092
(1.00) 		0.24
(1.00) 		0.0162
(1.00) 		0.894
(1.00) 		0.00899
(1.00)
Del Peak 10(4p15 2) 239 (60%) 158 0.000807
(0.579) 		0.00171
(1.00) 		6.52e-06
(0.00523) 		0.000341
(0.252) 		0.662
(1.00) 		0.0343
(1.00) 		0.0883
(1.00) 		0.0514
(1.00) 		0.325
(1.00) 		0.921
(1.00)
Del Peak 11(4q22 1) 217 (55%) 180 0.00685
(1.00) 		0.0579
(1.00) 		0.000102
(0.0782) 		0.00829
(1.00) 		0.123
(1.00) 		0.381
(1.00) 		0.0252
(1.00) 		0.00636
(1.00) 		0.219
(1.00) 		0.242
(1.00)
Del Peak 12(4q32 3) 248 (62%) 149 0.00967
(1.00) 		0.0253
(1.00) 		3.5e-07
(0.000286) 		0.000596
(0.432) 		0.101
(1.00) 		0.523
(1.00) 		0.0057
(1.00) 		0.036
(1.00) 		0.344
(1.00) 		0.0974
(1.00)
Del Peak 19(7q11 22) 37 (9%) 360 0.908
(1.00) 		0.405
(1.00) 		4.4e-05
(0.0342) 		0.829
(1.00) 		0.958
(1.00) 		0.75
(1.00) 		0.0463
(1.00) 		0.0644
(1.00) 		0.837
(1.00) 		0.524
(1.00)
Del Peak 22(9p23) 258 (65%) 139 0.00561
(1.00) 		0.00291
(1.00) 		1.97e-10
(1.64e-07) 		0.104
(1.00) 		0.146
(1.00) 		0.208
(1.00) 		0.0261
(1.00) 		0.0876
(1.00) 		0.986
(1.00) 		0.0652
(1.00)
Del Peak 23(9p21 3) 302 (76%) 95 0.372
(1.00) 		0.172
(1.00) 		4.99e-07
(0.000408) 		0.409
(1.00) 		0.695
(1.00) 		0.388
(1.00) 		0.164
(1.00) 		0.846
(1.00) 		0.852
(1.00) 		0.296
(1.00)
Del Peak 43(19p13 3) 173 (44%) 224 0.334
(1.00) 		0.0231
(1.00) 		1.38e-05
(0.0109) 		0.145
(1.00) 		0.0588
(1.00) 		0.251
(1.00) 		0.16
(1.00) 		0.0124
(1.00) 		0.0229
(1.00) 		0.0692
(1.00)
Del Peak 46(21q22 3) 224 (56%) 173 0.957
(1.00) 		0.193
(1.00) 		2.13e-08
(1.75e-05) 		0.00206
(1.00) 		0.396
(1.00) 		0.0991
(1.00) 		0.564
(1.00) 		0.302
(1.00) 		0.00395
(1.00) 		0.347
(1.00)
Del Peak 49(Xp22 2) 126 (32%) 271 0.599
(1.00) 		0.351
(1.00) 		0.000249
(0.187) 		0.0101
(1.00) 		0.277
(1.00) 		0.783
(1.00) 		0.14
(1.00) 		0.122
(1.00) 		0.122
(1.00) 		0.244
(1.00)
Amp Peak 1(1p34 2) 63 (16%) 334 0.028
(1.00) 		0.481
(1.00) 		0.000892
(0.637) 		0.644
(1.00) 		0.363
(1.00) 		0.619
(1.00) 		0.0484
(1.00) 		0.241
(1.00) 		0.222
(1.00) 		0.654
(1.00)
Amp Peak 5(3p11 1) 80 (20%) 317 0.0748
(1.00) 		0.844
(1.00) 		0.744
(1.00) 		0.957
(1.00) 		0.214
(1.00) 		0.0013
(0.913) 		0.0555
(1.00) 		0.444
(1.00) 		0.382
(1.00) 		0.772
(1.00)
Amp Peak 7(4q12) 93 (23%) 304 0.679
(1.00) 		0.759
(1.00) 		0.000353
(0.261) 		0.124
(1.00) 		0.356
(1.00) 		0.131
(1.00) 		0.555
(1.00) 		0.75
(1.00) 		0.163
(1.00) 		0.439
(1.00)
Amp Peak 10(6p12 1) 130 (33%) 267 0.557
(1.00) 		0.383
(1.00) 		0.0018
(1.00) 		0.168
(1.00) 		0.962
(1.00) 		0.3
(1.00) 		0.178
(1.00) 		0.841
(1.00) 		0.933
(1.00) 		0.464
(1.00)
Amp Peak 11(6q12) 117 (29%) 280 1
(1.00) 		0.873
(1.00) 		0.00114
(0.802) 		0.0454
(1.00) 		0.348
(1.00) 		0.408
(1.00) 		0.395
(1.00) 		0.236
(1.00) 		0.595
(1.00) 		0.214
(1.00)
Amp Peak 12(7p11 2) 193 (49%) 204 0.186
(1.00) 		0.0939
(1.00) 		0.00097
(0.687) 		0.00366
(1.00) 		0.687
(1.00) 		0.801
(1.00) 		0.076
(1.00) 		0.0148
(1.00) 		0.46
(1.00) 		0.157
(1.00)
Amp Peak 14(8p11 23) 184 (46%) 213 0.00812
(1.00) 		0.168
(1.00) 		0.0254
(1.00) 		0.0352
(1.00) 		0.192
(1.00) 		0.0988
(1.00) 		0.00631
(1.00) 		0.72
(1.00) 		0.131
(1.00) 		0.771
(1.00)
Amp Peak 15(8q24 21) 280 (71%) 117 0.871
(1.00) 		0.644
(1.00) 		0.554
(1.00) 		0.969
(1.00) 		0.917
(1.00) 		0.708
(1.00) 		0.734
(1.00) 		0.428
(1.00) 		0.392
(1.00) 		0.935
(1.00)
Amp Peak 16(9p24 1) 73 (18%) 324 0.375
(1.00) 		0.0295
(1.00) 		0.000354
(0.261) 		0.177
(1.00) 		0.0017
(1.00) 		0.00501
(1.00) 		0.0413
(1.00) 		0.00294
(1.00) 		0.461
(1.00) 		0.236
(1.00)
Amp Peak 17(9p13 3) 109 (27%) 288 0.17
(1.00) 		0.373
(1.00) 		0.043
(1.00) 		0.0387
(1.00) 		0.0708
(1.00) 		0.00898
(1.00) 		0.022
(1.00) 		0.188
(1.00) 		0.411
(1.00) 		0.973
(1.00)
Amp Peak 18(11q13 3) 143 (36%) 254 0.0697
(1.00) 		0.0306
(1.00) 		0.00486
(1.00) 		0.000518
(0.377) 		0.19
(1.00) 		0.0358
(1.00) 		0.0125
(1.00) 		0.139
(1.00) 		0.142
(1.00) 		0.214
(1.00)
Amp Peak 20(12q15) 144 (36%) 253 0.312
(1.00) 		0.527
(1.00) 		0.00531
(1.00) 		0.00136
(0.956) 		0.764
(1.00) 		0.524
(1.00) 		0.105
(1.00) 		0.0491
(1.00) 		0.509
(1.00) 		0.93
(1.00)
Amp Peak 21(13q34) 71 (18%) 326 0.964
(1.00) 		0.0489
(1.00) 		0.0384
(1.00) 		0.182
(1.00) 		0.87
(1.00) 		0.0834
(1.00) 		0.803
(1.00) 		0.407
(1.00) 		0.0664
(1.00) 		0.216
(1.00)
Amp Peak 22(14q13 3) 121 (30%) 276 0.345
(1.00) 		0.246
(1.00) 		0.127
(1.00) 		0.0969
(1.00) 		0.57
(1.00) 		0.00826
(1.00) 		0.617
(1.00) 		0.0847
(1.00) 		0.0275
(1.00) 		0.0972
(1.00)
Amp Peak 30(20q11 21) 229 (58%) 168 0.991
(1.00) 		0.844
(1.00) 		0.00052
(0.379) 		0.0132
(1.00) 		0.669
(1.00) 		0.588
(1.00) 		0.593
(1.00) 		0.549
(1.00) 		0.904
(1.00) 		0.519
(1.00)
Amp Peak 32(Xq28) 106 (27%) 291 0.633
(1.00) 		0.636
(1.00) 		0.039
(1.00) 		0.0815
(1.00) 		0.0701
(1.00) 		0.069
(1.00) 		0.136
(1.00) 		0.165
(1.00) 		0.502
(1.00) 		0.734
(1.00)
Del Peak 3(2p25 3) 37 (9%) 360 0.0461
(1.00) 		0.179
(1.00) 		0.0773
(1.00) 		0.37
(1.00) 		0.11
(1.00) 		0.838
(1.00) 		0.32
(1.00) 		0.226
(1.00) 		0.096
(1.00) 		0.0676
(1.00)
Del Peak 6(3p25 3) 313 (79%) 84 0.54
(1.00) 		0.176
(1.00) 		0.0278
(1.00) 		0.00221
(1.00) 		0.637
(1.00) 		0.18
(1.00) 		0.327
(1.00) 		0.00876
(1.00) 		0.759
(1.00) 		0.00743
(1.00)
Del Peak 9(3q11 1) 59 (15%) 338 0.759
(1.00) 		0.478
(1.00) 		0.117
(1.00) 		0.0538
(1.00) 		0.765
(1.00) 		0.282
(1.00) 		0.925
(1.00) 		0.674
(1.00) 		0.74
(1.00) 		0.891
(1.00)
Del Peak 16(6p25 3) 100 (25%) 297 0.22
(1.00) 		0.11
(1.00) 		0.00878
(1.00) 		0.00143
(1.00) 		0.393
(1.00) 		0.013
(1.00) 		0.01
(1.00) 		0.0204
(1.00) 		0.159
(1.00) 		0.181
(1.00)
Del Peak 17(6q22 31) 95 (24%) 302 0.0192
(1.00) 		0.00224
(1.00) 		0.00513
(1.00) 		0.000818
(0.586) 		0.629
(1.00) 		0.354
(1.00) 		0.0217
(1.00) 		0.0133
(1.00) 		0.194
(1.00) 		0.243
(1.00)
Del Peak 18(6q26) 103 (26%) 294 0.0659
(1.00) 		0.00298
(1.00) 		0.00234
(1.00) 		0.000727
(0.523) 		0.921
(1.00) 		0.69
(1.00) 		0.0687
(1.00) 		0.141
(1.00) 		0.149
(1.00) 		0.0889
(1.00)
Del Peak 20(7q36 3) 81 (20%) 316 0.187
(1.00) 		0.112
(1.00) 		0.00095
(0.675) 		0.274
(1.00) 		1
(1.00) 		0.315
(1.00) 		0.0928
(1.00) 		0.0698
(1.00) 		0.138
(1.00) 		0.163
(1.00)
Del Peak 21(8p23 2) 267 (67%) 130 0.864
(1.00) 		0.459
(1.00) 		0.000961
(0.682) 		0.173
(1.00) 		0.345
(1.00) 		0.141
(1.00) 		0.157
(1.00) 		0.072
(1.00) 		0.345
(1.00) 		0.285
(1.00)
Del Peak 29(11q22 1) 118 (30%) 279 0.493
(1.00) 		0.288
(1.00) 		0.0053
(1.00) 		0.0314
(1.00) 		0.103
(1.00) 		0.995
(1.00) 		0.259
(1.00) 		0.426
(1.00) 		0.219
(1.00) 		0.0584
(1.00)
Del Peak 30(11q25) 143 (36%) 254 0.798
(1.00) 		0.429
(1.00) 		0.0746
(1.00) 		0.333
(1.00) 		0.113
(1.00) 		0.908
(1.00) 		0.447
(1.00) 		0.406
(1.00) 		0.14
(1.00) 		0.189
(1.00)
Del Peak 31(12q24 31) 63 (16%) 334 0.965
(1.00) 		0.332
(1.00) 		0.426
(1.00) 		0.435
(1.00) 		0.323
(1.00) 		0.207
(1.00) 		0.9
(1.00) 		0.689
(1.00) 		0.282
(1.00) 		0.322
(1.00)
Del Peak 32(13q12 11) 260 (65%) 137 0.0547
(1.00) 		0.611
(1.00) 		0.0344
(1.00) 		0.164
(1.00) 		0.907
(1.00) 		0.268
(1.00) 		0.7
(1.00) 		0.214
(1.00) 		0.973
(1.00) 		1
(1.00)
Del Peak 33(13q14 2) 271 (68%) 126 0.0512
(1.00) 		0.0962
(1.00) 		0.00096
(0.682) 		0.053
(1.00) 		0.707
(1.00) 		0.682
(1.00) 		0.0281
(1.00) 		0.147
(1.00) 		0.905
(1.00) 		0.561
(1.00)
Del Peak 34(14q11 2) 140 (35%) 257 0.0546
(1.00) 		0.293
(1.00) 		0.163
(1.00) 		0.437
(1.00) 		0.206
(1.00) 		0.159
(1.00) 		0.00265
(1.00) 		0.00213
(1.00) 		0.252
(1.00) 		0.274
(1.00)
Del Peak 35(15q12) 131 (33%) 266 0.725
(1.00) 		0.228
(1.00) 		0.45
(1.00) 		0.347
(1.00) 		0.0717
(1.00) 		0.00798
(1.00) 		0.132
(1.00) 		0.356
(1.00) 		0.0723
(1.00) 		0.636
(1.00)
Del Peak 36(15q21 1) 124 (31%) 273 0.643
(1.00) 		0.242
(1.00) 		0.298
(1.00) 		0.969
(1.00) 		0.138
(1.00) 		0.00763
(1.00) 		0.156
(1.00) 		0.354
(1.00) 		0.228
(1.00) 		0.318
(1.00)
Del Peak 37(16p13 3) 148 (37%) 249 0.239
(1.00) 		0.245
(1.00) 		0.00525
(1.00) 		0.197
(1.00) 		0.149
(1.00) 		0.606
(1.00) 		0.531
(1.00) 		0.247
(1.00) 		0.618
(1.00) 		0.0677
(1.00)
Del Peak 38(16q23 1) 166 (42%) 231 0.942
(1.00) 		0.659
(1.00) 		0.0863
(1.00) 		0.271
(1.00) 		0.354
(1.00) 		0.761
(1.00) 		0.205
(1.00) 		0.0264
(1.00) 		0.535
(1.00) 		0.337
(1.00)
Del Peak 39(17p11 2) 202 (51%) 195 0.194
(1.00) 		0.401
(1.00) 		0.00185
(1.00) 		0.161
(1.00) 		0.15
(1.00) 		0.0182
(1.00) 		0.368
(1.00) 		0.86
(1.00) 		0.0666
(1.00) 		0.0313
(1.00)
Del Peak 41(17q25 3) 76 (19%) 321 0.00515
(1.00) 		0.0421
(1.00) 		0.000405
(0.299) 		0.0446
(1.00) 		0.622
(1.00) 		0.994
(1.00) 		0.13
(1.00) 		0.0021
(1.00) 		0.946
(1.00) 		0.111
(1.00)
Del Peak 42(18q23) 179 (45%) 218 0.508
(1.00) 		0.788
(1.00) 		0.502
(1.00) 		0.898
(1.00) 		0.801
(1.00) 		0.397
(1.00) 		0.23
(1.00) 		0.115
(1.00) 		0.773
(1.00) 		0.502
(1.00)
Del Peak 45(21q21 1) 189 (48%) 208 0.481
(1.00) 		0.135
(1.00) 		0.0117
(1.00) 		0.0293
(1.00) 		0.585
(1.00) 		0.89
(1.00) 		0.996
(1.00) 		0.815
(1.00) 		0.0562
(1.00) 		0.0687
(1.00)
Del Peak 47(22q11 21) 68 (17%) 329 0.0904
(1.00) 		0.0093
(1.00) 		0.0672
(1.00) 		0.0841
(1.00) 		0.145
(1.00) 		0.129
(1.00) 		0.598
(1.00) 		0.748
(1.00) 		0.172
(1.00) 		0.126
(1.00)
'Amp Peak 2(1q21.2) mutation analysis' versus 'CN_CNMF'

P value = 1.98e-07 (Fisher's exact test), Q value = 0.00016

Table S1.  Gene #2: 'Amp Peak 2(1q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 2(1Q21.2) MUTATED 57 92 56
AMP PEAK 2(1Q21.2) WILD-TYPE 86 37 69

Figure S1.  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 = 0.23

Table S2.  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 S2.  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 = 3.18e-13 (Fisher's exact test), Q value = 2.7e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 3(2P16.1) MUTATED 49 102 65
AMP PEAK 3(2P16.1) WILD-TYPE 94 27 60

Figure S3.  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 = 5.83e-05 (Fisher's exact test), Q value = 0.045

Table S4.  Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 3(2P16.1) MUTATED 43 61 31
AMP PEAK 3(2P16.1) WILD-TYPE 55 22 38

Figure S4.  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 = 0.25

Table S5.  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 S5.  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 = 6.52e-06 (Fisher's exact test), Q value = 0.0052

Table S6.  Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 4(2Q31.2) MUTATED 30 63 39
AMP PEAK 4(2Q31.2) WILD-TYPE 113 66 86

Figure S6.  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 = 1.99e-07 (Fisher's exact test), Q value = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 4(2Q31.2) MUTATED 23 48 14
AMP PEAK 4(2Q31.2) WILD-TYPE 75 35 55

Figure S7.  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 = 0.014

Table S8.  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 S8.  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 = 7.05e-12 (Fisher's exact test), Q value = 5.9e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 6(3Q26.33) MUTATED 113 129 122
AMP PEAK 6(3Q26.33) WILD-TYPE 30 0 3

Figure S9.  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 = 6.69e-07 (Fisher's exact test), Q value = 0.00055

Table S10.  Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 6(3Q26.33) MUTATED 79 83 67
AMP PEAK 6(3Q26.33) WILD-TYPE 19 0 2

Figure S10.  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 = 0.03

Table S11.  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 S11.  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 S12.  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 S12.  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 = 1.37e-05 (Fisher's exact test), Q value = 0.011

Table S13.  Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 176 118
AMP PEAK 6(3Q26.33) MUTATED 53 151 116
AMP PEAK 6(3Q26.33) WILD-TYPE 0 25 2

Figure S13.  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 = 1.07e-05 (Fisher's exact test), Q value = 0.0085

Table S14.  Gene #8: 'Amp Peak 8(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 8(5P15.33) MUTATED 99 100 115
AMP PEAK 8(5P15.33) WILD-TYPE 44 29 10

Figure S14.  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 = 7.58e-10 (Fisher's exact test), Q value = 6.3e-07

Table S15.  Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 9(5P12) MUTATED 70 84 107
AMP PEAK 9(5P12) WILD-TYPE 73 45 18

Figure S15.  Get High-res Image Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 13(7q21.2) mutation analysis' versus 'CN_CNMF'

P value = 5.34e-10 (Fisher's exact test), Q value = 4.4e-07

Table S16.  Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 13(7Q21.2) MUTATED 51 96 62
AMP PEAK 13(7Q21.2) WILD-TYPE 92 33 63

Figure S16.  Get High-res Image Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 13(7q21.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.01

Table S17.  Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 13(7Q21.2) MUTATED 35 58 30
AMP PEAK 13(7Q21.2) WILD-TYPE 63 25 39

Figure S17.  Get High-res Image Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 19(12p13.33) mutation analysis' versus 'CN_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0098

Table S18.  Gene #19: 'Amp Peak 19(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 19(12P13.33) MUTATED 51 83 64
AMP PEAK 19(12P13.33) WILD-TYPE 92 46 61

Figure S18.  Get High-res Image Gene #19: 'Amp Peak 19(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 23(15q26.3) mutation analysis' versus 'CN_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.012

Table S19.  Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 23(15Q26.3) MUTATED 30 61 48
AMP PEAK 23(15Q26.3) WILD-TYPE 113 68 77

Figure S19.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 23(15q26.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.39e-06 (Fisher's exact test), Q value = 0.0075

Table S20.  Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 23(15Q26.3) MUTATED 16 40 27
AMP PEAK 23(15Q26.3) WILD-TYPE 82 43 42

Figure S20.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 24(17q25.1) mutation analysis' versus 'CN_CNMF'

P value = 6.01e-07 (Fisher's exact test), Q value = 0.00049

Table S21.  Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 24(17Q25.1) MUTATED 46 83 62
AMP PEAK 24(17Q25.1) WILD-TYPE 97 46 63

Figure S21.  Get High-res Image Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 24(17q25.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.017

Table S22.  Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 24(17Q25.1) MUTATED 34 55 25
AMP PEAK 24(17Q25.1) WILD-TYPE 64 28 44

Figure S22.  Get High-res Image Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 25(18p11.32) mutation analysis' versus 'CN_CNMF'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.019

Table S23.  Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 25(18P11.32) MUTATED 32 63 42
AMP PEAK 25(18P11.32) WILD-TYPE 111 66 83

Figure S23.  Get High-res Image Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 25(18p11.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.096

Table S24.  Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 25(18P11.32) MUTATED 18 38 28
AMP PEAK 25(18P11.32) WILD-TYPE 80 45 41

Figure S24.  Get High-res Image Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 26(18q11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.011

Table S25.  Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 26(18Q11.2) MUTATED 26 57 43
AMP PEAK 26(18Q11.2) WILD-TYPE 117 72 82

Figure S25.  Get High-res Image Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 27(19q12) mutation analysis' versus 'CN_CNMF'

P value = 4.07e-06 (Fisher's exact test), Q value = 0.0033

Table S26.  Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 27(19Q12) MUTATED 45 77 45
AMP PEAK 27(19Q12) WILD-TYPE 98 52 80

Figure S26.  Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 28(19q13.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.15

Table S27.  Gene #28: 'Amp Peak 28(19q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 28(19Q13.2) MUTATED 48 74 48
AMP PEAK 28(19Q13.2) WILD-TYPE 95 55 77

Figure S27.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 29(20p12.2) mutation analysis' versus 'CN_CNMF'

P value = 8.92e-08 (Fisher's exact test), Q value = 7.3e-05

Table S28.  Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 29(20P12.2) MUTATED 53 92 66
AMP PEAK 29(20P12.2) WILD-TYPE 90 37 59

Figure S28.  Get High-res Image Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 29(20p12.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.12

Table S29.  Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
AMP PEAK 29(20P12.2) MUTATED 42 60 33
AMP PEAK 29(20P12.2) WILD-TYPE 56 23 36

Figure S29.  Get High-res Image Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 31(22q11.21) mutation analysis' versus 'CN_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.22

Table S30.  Gene #31: 'Amp Peak 31(22q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
AMP PEAK 31(22Q11.21) MUTATED 54 80 65
AMP PEAK 31(22Q11.21) WILD-TYPE 89 49 60

Figure S30.  Get High-res Image Gene #31: 'Amp Peak 31(22q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 1(1p36.22) mutation analysis' versus 'MRNA_CNMF'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0012

Table S31.  Gene #33: 'Del Peak 1(1p36.22) 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(1P36.22) MUTATED 9 37 13 10
DEL PEAK 1(1P36.22) WILD-TYPE 34 13 17 21

Figure S31.  Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 1(1p36.22) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.78e-08 (Fisher's exact test), Q value = 1.5e-05

Table S32.  Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 1(1P36.22) MUTATED 11 41 17
DEL PEAK 1(1P36.22) WILD-TYPE 17 13 55

Figure S32.  Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.22) mutation analysis' versus 'CN_CNMF'

P value = 1.61e-28 (Fisher's exact test), Q value = 1.4e-25

Table S33.  Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 1(1P36.22) MUTATED 34 107 31
DEL PEAK 1(1P36.22) WILD-TYPE 109 22 94

Figure S33.  Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 1(1p36.22) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.1e-14 (Fisher's exact test), Q value = 1.8e-11

Table S34.  Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 1(1P36.22) MUTATED 17 61 22
DEL PEAK 1(1P36.22) WILD-TYPE 81 22 47

Figure S34.  Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.22) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.09e-09 (Fisher's exact test), Q value = 9e-07

Table S35.  Gene #33: 'Del Peak 1(1p36.22) 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(1P36.22) MUTATED 16 60 27 12
DEL PEAK 1(1P36.22) WILD-TYPE 44 20 52 26

Figure S35.  Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.22) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.35e-08 (Fisher's exact test), Q value = 1.1e-05

Table S36.  Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
DEL PEAK 1(1P36.22) MUTATED 36 61 18
DEL PEAK 1(1P36.22) WILD-TYPE 80 25 37

Figure S36.  Get High-res Image Gene #33: 'Del Peak 1(1p36.22) 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 = 0.18

Table S37.  Gene #34: '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 S37.  Get High-res Image Gene #34: '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 = 1.23e-15 (Fisher's exact test), Q value = 1e-12

Table S38.  Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 2(1P13.2) MUTATED 35 93 44
DEL PEAK 2(1P13.2) WILD-TYPE 108 36 81

Figure S38.  Get High-res Image Gene #34: '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 = 5.74e-09 (Fisher's exact test), Q value = 4.8e-06

Table S39.  Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 2(1P13.2) MUTATED 20 54 28
DEL PEAK 2(1P13.2) WILD-TYPE 78 29 41

Figure S39.  Get High-res Image Gene #34: '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 S40.  Gene #34: '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 S40.  Get High-res Image Gene #34: '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 = 0.055

Table S41.  Gene #34: '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 S41.  Get High-res Image Gene #34: '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 = 0.000271 (Fisher's exact test), Q value = 0.2

Table S42.  Gene #36: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 4(2Q22.1) MUTATED 22 47 36
DEL PEAK 4(2Q22.1) WILD-TYPE 121 82 89

Figure S42.  Get High-res Image Gene #36: '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 = 0.18

Table S43.  Gene #37: '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 S43.  Get High-res Image Gene #37: '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 = 0.037

Table S44.  Gene #37: '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 S44.  Get High-res Image Gene #37: '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 = 1.7e-12 (Fisher's exact test), Q value = 1.4e-09

Table S45.  Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 5(2Q36.2) MUTATED 23 74 35
DEL PEAK 5(2Q36.2) WILD-TYPE 120 55 90

Figure S45.  Get High-res Image Gene #37: '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 = 2.14e-06 (Fisher's exact test), Q value = 0.0017

Table S46.  Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 5(2Q36.2) MUTATED 17 44 25
DEL PEAK 5(2Q36.2) WILD-TYPE 81 39 44

Figure S46.  Get High-res Image Gene #37: '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 = 0.065

Table S47.  Gene #37: '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 S47.  Get High-res Image Gene #37: '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 = 0.0049

Table S48.  Gene #37: '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 S48.  Get High-res Image Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.67e-06 (Fisher's exact test), Q value = 0.0022

Table S49.  Gene #39: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 7(3P13) MUTATED 105 119 116
DEL PEAK 7(3P13) WILD-TYPE 38 10 9

Figure S49.  Get High-res Image Gene #39: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.03e-05 (Fisher's exact test), Q value = 0.024

Table S50.  Gene #40: 'Del Peak 8(3p12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 8(3P12.3) MUTATED 103 116 113
DEL PEAK 8(3P12.3) WILD-TYPE 40 13 12

Figure S50.  Get High-res Image Gene #40: 'Del Peak 8(3p12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 6.52e-06 (Fisher's exact test), Q value = 0.0052

Table S51.  Gene #42: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 10(4P15.2) MUTATED 70 99 70
DEL PEAK 10(4P15.2) WILD-TYPE 73 30 55

Figure S51.  Get High-res Image Gene #42: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000102 (Fisher's exact test), Q value = 0.078

Table S52.  Gene #43: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 11(4Q22.1) MUTATED 65 90 62
DEL PEAK 11(4Q22.1) WILD-TYPE 78 39 63

Figure S52.  Get High-res Image Gene #43: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.5e-07 (Fisher's exact test), Q value = 0.00029

Table S53.  Gene #44: 'Del Peak 12(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 12(4Q32.3) MUTATED 72 104 72
DEL PEAK 12(4Q32.3) WILD-TYPE 71 25 53

Figure S53.  Get High-res Image Gene #44: 'Del Peak 12(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0023

Table S54.  Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 13(4Q35.2) MUTATED 76 104 73
DEL PEAK 13(4Q35.2) WILD-TYPE 67 25 52

Figure S54.  Get High-res Image Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000124 (Fisher's exact test), Q value = 0.094

Table S55.  Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 13(4Q35.2) MUTATED 47 65 42
DEL PEAK 13(4Q35.2) WILD-TYPE 51 18 27

Figure S55.  Get High-res Image Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 2.03e-12 (Fisher's exact test), Q value = 1.7e-09

Table S56.  Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 14(5Q11.2) MUTATED 73 108 109
DEL PEAK 14(5Q11.2) WILD-TYPE 70 21 16

Figure S56.  Get High-res Image Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000192 (Fisher's exact test), Q value = 0.15

Table S57.  Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 14(5Q11.2) MUTATED 57 69 56
DEL PEAK 14(5Q11.2) WILD-TYPE 41 14 13

Figure S57.  Get High-res Image Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 8.06e-05 (Fisher's exact test), Q value = 0.062

Table S58.  Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 176 118
DEL PEAK 14(5Q11.2) MUTATED 41 115 103
DEL PEAK 14(5Q11.2) WILD-TYPE 12 61 15

Figure S58.  Get High-res Image Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(5q31.1) mutation analysis' versus 'CN_CNMF'

P value = 5.7e-09 (Fisher's exact test), Q value = 4.7e-06

Table S59.  Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 15(5Q31.1) MUTATED 86 111 111
DEL PEAK 15(5Q31.1) WILD-TYPE 57 18 14

Figure S59.  Get High-res Image Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 15(5q31.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.023

Table S60.  Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 15(5Q31.1) MUTATED 63 71 63
DEL PEAK 15(5Q31.1) WILD-TYPE 35 12 6

Figure S60.  Get High-res Image Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 19(7q11.22) mutation analysis' versus 'CN_CNMF'

P value = 4.4e-05 (Fisher's exact test), Q value = 0.034

Table S61.  Gene #51: 'Del Peak 19(7q11.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 19(7Q11.22) MUTATED 11 3 23
DEL PEAK 19(7Q11.22) WILD-TYPE 132 126 102

Figure S61.  Get High-res Image Gene #51: 'Del Peak 19(7q11.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 22(9p23) mutation analysis' versus 'CN_CNMF'

P value = 1.97e-10 (Fisher's exact test), Q value = 1.6e-07

Table S62.  Gene #54: 'Del Peak 22(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 22(9P23) MUTATED 74 75 109
DEL PEAK 22(9P23) WILD-TYPE 69 54 16

Figure S62.  Get High-res Image Gene #54: 'Del Peak 22(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 23(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 4.99e-07 (Fisher's exact test), Q value = 0.00041

Table S63.  Gene #55: 'Del Peak 23(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 23(9P21.3) MUTATED 92 96 114
DEL PEAK 23(9P21.3) WILD-TYPE 51 33 11

Figure S63.  Get High-res Image Gene #55: 'Del Peak 23(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S64.  Gene #56: 'Del Peak 24(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 24(9Q21.11) MUTATED 28 12 19 15
DEL PEAK 24(9Q21.11) WILD-TYPE 15 38 11 16

Figure S64.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 4.92e-05 (Fisher's exact test), Q value = 0.038

Table S65.  Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 24(9Q21.11) MUTATED 16 13 45
DEL PEAK 24(9Q21.11) WILD-TYPE 12 41 27

Figure S65.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 5.97e-11 (Fisher's exact test), Q value = 5e-08

Table S66.  Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 24(9Q21.11) MUTATED 69 35 87
DEL PEAK 24(9Q21.11) WILD-TYPE 74 94 38

Figure S66.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00093

Table S67.  Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 24(9Q21.11) MUTATED 54 22 46
DEL PEAK 24(9Q21.11) WILD-TYPE 44 61 23

Figure S67.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 4.44e-06 (Fisher's exact test), Q value = 0.0036

Table S68.  Gene #56: 'Del Peak 24(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 24(9Q21.11) MUTATED 33 19 48 22
DEL PEAK 24(9Q21.11) WILD-TYPE 27 61 31 16

Figure S68.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 2.4e-07 (Fisher's exact test), Q value = 2e-04

Table S69.  Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
DEL PEAK 24(9Q21.11) MUTATED 64 21 37
DEL PEAK 24(9Q21.11) WILD-TYPE 52 65 18

Figure S69.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000283 (Fisher's exact test), Q value = 0.21

Table S70.  Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 176 118
DEL PEAK 24(9Q21.11) MUTATED 13 90 67
DEL PEAK 24(9Q21.11) WILD-TYPE 40 86 51

Figure S70.  Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.8e-05 (Fisher's exact test), Q value = 0.037

Table S71.  Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 25(10P15.3) MUTATED 45 75 58
DEL PEAK 25(10P15.3) WILD-TYPE 98 54 67

Figure S71.  Get High-res Image Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 9.6e-05 (Fisher's exact test), Q value = 0.074

Table S72.  Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 25(10P15.3) MUTATED 34 54 27
DEL PEAK 25(10P15.3) WILD-TYPE 64 29 42

Figure S72.  Get High-res Image Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S73.  Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 26(10P15.1) MUTATED 43 71 54
DEL PEAK 26(10P15.1) WILD-TYPE 100 58 71

Figure S73.  Get High-res Image Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 26(10p15.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.03e-06 (Fisher's exact test), Q value = 0.0033

Table S74.  Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 26(10P15.1) MUTATED 32 55 23
DEL PEAK 26(10P15.1) WILD-TYPE 66 28 46

Figure S74.  Get High-res Image Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 26(10p15.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000259 (Fisher's exact test), Q value = 0.19

Table S75.  Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 80 79 38
DEL PEAK 26(10P15.1) MUTATED 17 48 32 10
DEL PEAK 26(10P15.1) WILD-TYPE 43 32 47 28

Figure S75.  Get High-res Image Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 27(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.017

Table S76.  Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 27(10Q23.31) MUTATED 58 87 58
DEL PEAK 27(10Q23.31) WILD-TYPE 85 42 67

Figure S76.  Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 27(10q23.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.0017

Table S77.  Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 27(10Q23.31) MUTATED 34 60 33
DEL PEAK 27(10Q23.31) WILD-TYPE 64 23 36

Figure S77.  Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 27(10q23.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.079

Table S78.  Gene #59: 'Del Peak 27(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 27(10Q23.31) MUTATED 22 57 35 16
DEL PEAK 27(10Q23.31) WILD-TYPE 38 23 44 22

Figure S78.  Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 27(10q23.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.021

Table S79.  Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

Figure S79.  Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.001

Table S80.  Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 28(11P15.5) MUTATED 49 53 81
DEL PEAK 28(11P15.5) WILD-TYPE 94 76 44

Figure S80.  Get High-res Image Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 28(11p15.5) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.016

Table S81.  Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 47 49 40
DEL PEAK 28(11P15.5) MUTATED 29 17 36 10
DEL PEAK 28(11P15.5) WILD-TYPE 29 30 13 30

Figure S81.  Get High-res Image Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 40(17q11.2) mutation analysis' versus 'MRNA_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.01

Table S82.  Gene #72: 'Del Peak 40(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 40(17Q11.2) MUTATED 21 3 11 7
DEL PEAK 40(17Q11.2) WILD-TYPE 22 47 19 24

Figure S82.  Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 40(17q11.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.44e-05 (Fisher's exact test), Q value = 0.05

Table S83.  Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 40(17Q11.2) MUTATED 9 4 29
DEL PEAK 40(17Q11.2) WILD-TYPE 19 50 43

Figure S83.  Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(17q11.2) mutation analysis' versus 'CN_CNMF'

P value = 3.04e-08 (Fisher's exact test), Q value = 2.5e-05

Table S84.  Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 40(17Q11.2) MUTATED 40 10 46
DEL PEAK 40(17Q11.2) WILD-TYPE 103 119 79

Figure S84.  Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 40(17q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.093

Table S85.  Gene #72: 'Del Peak 40(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 40(17Q11.2) MUTATED 20 6 23 13
DEL PEAK 40(17Q11.2) WILD-TYPE 40 74 56 25

Figure S85.  Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 40(17q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.16e-06 (Fisher's exact test), Q value = 0.0057

Table S86.  Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
DEL PEAK 40(17Q11.2) MUTATED 39 6 17
DEL PEAK 40(17Q11.2) WILD-TYPE 77 80 38

Figure S86.  Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 43(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.011

Table S87.  Gene #75: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 43(19P13.3) MUTATED 48 49 76
DEL PEAK 43(19P13.3) WILD-TYPE 95 80 49

Figure S87.  Get High-res Image Gene #75: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 44(19q13.33) mutation analysis' versus 'CN_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.13

Table S88.  Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 44(19Q13.33) MUTATED 22 48 36
DEL PEAK 44(19Q13.33) WILD-TYPE 121 81 89

Figure S88.  Get High-res Image Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 44(19q13.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.14

Table S89.  Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 44(19Q13.33) MUTATED 12 30 23
DEL PEAK 44(19Q13.33) WILD-TYPE 86 53 46

Figure S89.  Get High-res Image Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 46(21q22.3) mutation analysis' versus 'CN_CNMF'

P value = 2.13e-08 (Fisher's exact test), Q value = 1.8e-05

Table S90.  Gene #78: 'Del Peak 46(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 46(21Q22.3) MUTATED 53 91 80
DEL PEAK 46(21Q22.3) WILD-TYPE 90 38 45

Figure S90.  Get High-res Image Gene #78: 'Del Peak 46(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 48(22q13.32) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.21

Table S91.  Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 50 30 31
DEL PEAK 48(22Q13.32) MUTATED 9 7 7 18
DEL PEAK 48(22Q13.32) WILD-TYPE 34 43 23 13

Figure S91.  Get High-res Image Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 48(22q13.32) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 8.68e-05 (Fisher's exact test), Q value = 0.067

Table S92.  Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
DEL PEAK 48(22Q13.32) MUTATED 17 9 15
DEL PEAK 48(22Q13.32) WILD-TYPE 11 45 57

Figure S92.  Get High-res Image Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 49(Xp22.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.19

Table S93.  Gene #81: 'Del Peak 49(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 49(XP22.2) MUTATED 28 53 45
DEL PEAK 49(XP22.2) WILD-TYPE 115 76 80

Figure S93.  Get High-res Image Gene #81: 'Del Peak 49(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 50(Xp21.1) mutation analysis' versus 'CN_CNMF'

P value = 5.39e-05 (Fisher's exact test), Q value = 0.042

Table S94.  Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 50(XP21.1) MUTATED 27 55 45
DEL PEAK 50(XP21.1) WILD-TYPE 116 74 80

Figure S94.  Get High-res Image Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 50(Xp21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.18

Table S95.  Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 50(XP21.1) MUTATED 18 36 29
DEL PEAK 50(XP21.1) WILD-TYPE 80 47 40

Figure S95.  Get High-res Image Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 51(Xp11.3) mutation analysis' versus 'CN_CNMF'

P value = 9.19e-06 (Fisher's exact test), Q value = 0.0073

Table S96.  Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 51(XP11.3) MUTATED 26 58 41
DEL PEAK 51(XP11.3) WILD-TYPE 117 71 84

Figure S96.  Get High-res Image Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 51(Xp11.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.09e-05 (Fisher's exact test), Q value = 0.032

Table S97.  Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 51(XP11.3) MUTATED 16 38 26
DEL PEAK 51(XP11.3) WILD-TYPE 82 45 43

Figure S97.  Get High-res Image Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 52(Xq22.3) mutation analysis' versus 'CN_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.015

Table S98.  Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
DEL PEAK 52(XQ22.3) MUTATED 18 31 46
DEL PEAK 52(XQ22.3) WILD-TYPE 125 98 79

Figure S98.  Get High-res Image Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 52(Xq22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.19

Table S99.  Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
DEL PEAK 52(XQ22.3) MUTATED 10 20 25
DEL PEAK 52(XQ22.3) WILD-TYPE 88 63 44

Figure S99.  Get High-res Image Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_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 = 397

  • Number of copy number variation regions = 84

  • 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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