Correlation between copy number variation genes and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1125QTD
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/C1125QTD
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 72 peak regions and 8 molecular subtypes across 322 patients, 107 significant findings detected with Q value < 0.25.

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

  • Amp Peak 2(2q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • Amp Peak 4(2q32.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • Amp Peak 6(5p15.33) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 7(5p12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 8(6p12.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 10(7p11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 11(7q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 13(8q11.21) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 14(8q24.21) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 19(11q13.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 20(12p13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 21(12q15) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 22(13q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 23(14q11.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 24(15q26.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 25(17q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 26(18p11.31) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 28(20q11.22) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 29(Xq28) cnvs correlated to 'CN_CNMF'.

  • Del Peak 1(1p36.13) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

  • Del Peak 5(2q36.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 6(3p24.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 8(3p12.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 9(4p16.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

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

  • Del Peak 14(5q35.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 15(6p25.3) cnvs correlated to 'METHLYATION_CNMF'.

  • Del Peak 18(8p23.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 19(9p23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 20(9p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 21(9q21.11) cnvs correlated to 'CN_CNMF'.

  • Del Peak 23(10p15.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 24(10p11.21) cnvs correlated to 'CN_CNMF'.

  • Del Peak 26(11p15.4) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 27(11q23.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 29(13q12.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 30(13q14.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 32(14q32.32) cnvs correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 34(16q12.1) cnvs correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Del Peak 35(16q23.3) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 37(18q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 38(18q23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 40(19q13.43) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 41(Xp21.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 42(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 43(Xq21.33) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 72 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 107 significant findings detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Chi-square test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Amp Peak 14(8q24 21) 232 (72%) 90 5.76e-08
(3.07e-05) 		0.000106
(0.0515) 		0.231
(1.00) 		0.58
(1.00) 		0.000102
(0.05) 		0.000135
(0.0654) 		0.0442
(1.00) 		0.000169
(0.0817)
Amp Peak 1(1q21 2) 76 (24%) 246 1.21e-07
(6.4e-05) 		2.63e-08
(1.42e-05) 		0.838
(1.00) 		0.359
(1.00) 		0.000509
(0.24) 		0.00316
(1.00) 		0.000103
(0.0502) 		0.272
(1.00)
Del Peak 30(13q14 2) 137 (43%) 185 3.1e-07
(0.000163) 		5.88e-07
(0.000306) 		0.661
(1.00) 		0.26
(1.00) 		5.7e-05
(0.0283) 		6.46e-05
(0.032) 		0.0431
(1.00) 		0.568
(1.00)
Del Peak 34(16q12 1) 54 (17%) 268 0.0731
(1.00) 		1.13e-07
(5.97e-05) 		0.399
(1.00) 		0.0768
(1.00) 		7.1e-08
(3.78e-05) 		3.91e-07
(0.000205) 		0.00037
(0.175) 		0.00585
(1.00)
Amp Peak 5(3q26 33) 242 (75%) 80 1.29e-09
(7.09e-07) 		3.26e-05
(0.0163) 		0.435
(1.00) 		0.263
(1.00) 		0.000829
(0.382) 		0.000288
(0.137) 		0.00356
(1.00) 		0.406
(1.00)
Del Peak 1(1p36 13) 68 (21%) 254 1.48e-10
(8.22e-08) 		5.38e-15
(3.05e-12) 		0.00322
(1.00) 		0.84
(1.00) 		3.03e-05
(0.0152) 		0.000716
(0.332) 		0.0131
(1.00) 		0.0668
(1.00)
Del Peak 2(1p13 2) 81 (25%) 241 2.77e-10
(1.53e-07) 		8.62e-10
(4.73e-07) 		0.00301
(1.00) 		0.0475
(1.00) 		0.00546
(1.00) 		0.0927
(1.00) 		0.000181
(0.0869) 		0.97
(1.00)
Del Peak 14(5q35 3) 127 (39%) 195 4.01e-15
(2.28e-12) 		4.25e-14
(2.4e-11) 		0.243
(1.00) 		0.187
(1.00) 		0.0146
(1.00) 		0.000477
(0.225) 		0.13
(1.00) 		0.663
(1.00)
Del Peak 27(11q23 1) 153 (48%) 169 1.37e-14
(7.76e-12) 		8.45e-07
(0.000435) 		0.358
(1.00) 		0.453
(1.00) 		0.000815
(0.377) 		0.00023
(0.11) 		0.207
(1.00) 		0.182
(1.00)
Del Peak 32(14q32 32) 49 (15%) 273 0.285
(1.00) 		1.42e-07
(7.5e-05) 		0.317
(1.00) 		0.507
(1.00) 		0.000242
(0.116) 		9.8e-05
(0.048) 		0.115
(1.00) 		0.126
(1.00)
Amp Peak 2(2q11 2) 69 (21%) 253 3.48e-06
(0.00178) 		1.71e-08
(9.26e-06) 		0.935
(1.00) 		0.188
(1.00) 		0.0119
(1.00) 		0.0807
(1.00) 		0.045
(1.00) 		0.429
(1.00)
Amp Peak 3(2q31 2) 67 (21%) 255 8.38e-10
(4.61e-07) 		9.37e-09
(5.09e-06) 		0.117
(1.00) 		0.359
(1.00) 		0.318
(1.00) 		0.11
(1.00) 		0.367
(1.00) 		0.0818
(1.00)
Amp Peak 4(2q32 2) 59 (18%) 263 7.97e-07
(0.000411) 		5.3e-08
(2.84e-05) 		0.0495
(1.00) 		0.427
(1.00) 		0.169
(1.00) 		0.0513
(1.00) 		0.0433
(1.00) 		0.129
(1.00)
Amp Peak 10(7p11 2) 137 (43%) 185 1.91e-08
(1.03e-05) 		6.87e-07
(0.000356) 		0.935
(1.00) 		0.75
(1.00) 		0.5
(1.00) 		0.923
(1.00) 		0.405
(1.00) 		0.197
(1.00)
Amp Peak 11(7q22 1) 114 (35%) 208 3.1e-11
(1.73e-08) 		5.46e-08
(2.91e-05) 		0.617
(1.00) 		1
(1.00) 		0.235
(1.00) 		0.335
(1.00) 		0.0689
(1.00) 		0.101
(1.00)
Amp Peak 20(12p13 33) 109 (34%) 213 5.52e-11
(3.07e-08) 		1.28e-05
(0.0065) 		0.0836
(1.00) 		0.413
(1.00) 		0.00912
(1.00) 		0.00101
(0.462) 		0.00247
(1.00) 		0.814
(1.00)
Amp Peak 22(13q22 1) 68 (21%) 254 4.16e-07
(0.000218) 		8.43e-05
(0.0416) 		0.00708
(1.00) 		0.335
(1.00) 		0.233
(1.00) 		0.0924
(1.00) 		0.551
(1.00) 		0.409
(1.00)
Amp Peak 25(17q12) 56 (17%) 266 4.94e-05
(0.0246) 		0.000112
(0.0541) 		0.944
(1.00) 		0.961
(1.00) 		0.0168
(1.00) 		0.0308
(1.00) 		0.0253
(1.00) 		0.399
(1.00)
Del Peak 5(2q36 2) 96 (30%) 226 0.000122
(0.0591) 		5.69e-06
(0.0029) 		0.248
(1.00) 		0.269
(1.00) 		0.000636
(0.298) 		0.00125
(0.571) 		0.0614
(1.00) 		0.0106
(1.00)
Del Peak 6(3p24 1) 239 (74%) 83 3.25e-27
(1.87e-24) 		3.93e-08
(2.11e-05) 		0.183
(1.00) 		0.247
(1.00) 		0.0707
(1.00) 		0.369
(1.00) 		0.404
(1.00) 		0.0983
(1.00)
Del Peak 7(3p14 2) 242 (75%) 80 3.41e-27
(1.96e-24) 		5.71e-07
(0.000298) 		0.137
(1.00) 		0.603
(1.00) 		0.115
(1.00) 		0.161
(1.00) 		0.895
(1.00) 		0.122
(1.00)
Del Peak 8(3p12 2) 228 (71%) 94 3.11e-25
(1.79e-22) 		4.04e-09
(2.2e-06) 		0.843
(1.00) 		0.784
(1.00) 		0.241
(1.00) 		0.463
(1.00) 		0.541
(1.00) 		0.122
(1.00)
Del Peak 9(4p16 3) 137 (43%) 185 1.38e-14
(7.8e-12) 		1.5e-05
(0.00756) 		0.0156
(1.00) 		0.711
(1.00) 		0.307
(1.00) 		0.161
(1.00) 		0.111
(1.00) 		0.594
(1.00)
Del Peak 10(4p15 2) 138 (43%) 184 7.36e-16
(4.2e-13) 		5.98e-07
(0.000311) 		0.0207
(1.00) 		0.326
(1.00) 		0.0406
(1.00) 		0.0129
(1.00) 		0.0214
(1.00) 		0.687
(1.00)
Del Peak 11(4q22 1) 102 (32%) 220 5.42e-12
(3.04e-09) 		6.5e-07
(0.000337) 		0.0244
(1.00) 		0.769
(1.00) 		0.371
(1.00) 		0.205
(1.00) 		0.293
(1.00) 		0.71
(1.00)
Del Peak 12(4q35 2) 131 (41%) 191 4e-08
(2.14e-05) 		2.97e-05
(0.0149) 		0.00405
(1.00) 		0.602
(1.00) 		0.275
(1.00) 		0.353
(1.00) 		0.296
(1.00) 		0.292
(1.00)
Del Peak 13(5q11 2) 134 (42%) 188 1.65e-16
(9.45e-14) 		1.35e-12
(7.57e-10) 		0.0952
(1.00) 		0.786
(1.00) 		0.0401
(1.00) 		0.000767
(0.355) 		0.076
(1.00) 		0.397
(1.00)
Del Peak 18(8p23 2) 183 (57%) 139 4.99e-12
(2.8e-09) 		3.84e-05
(0.0191) 		0.524
(1.00) 		0.237
(1.00) 		0.0166
(1.00) 		0.00353
(1.00) 		0.0584
(1.00) 		0.00355
(1.00)
Del Peak 19(9p23) 151 (47%) 171 6.45e-13
(3.63e-10) 		5.42e-09
(2.95e-06) 		0.174
(1.00) 		0.845
(1.00) 		0.74
(1.00) 		0.493
(1.00) 		0.652
(1.00) 		0.225
(1.00)
Del Peak 20(9p21 3) 189 (59%) 133 3.52e-10
(1.94e-07) 		2.83e-09
(1.54e-06) 		0.399
(1.00) 		0.646
(1.00) 		0.39
(1.00) 		0.462
(1.00) 		0.958
(1.00) 		0.62
(1.00)
Del Peak 26(11p15 4) 102 (32%) 220 3.91e-06
(0.002) 		0.000523
(0.246) 		0.426
(1.00) 		0.598
(1.00) 		0.00228
(1.00) 		0.0071
(1.00) 		0.00335
(1.00) 		0.196
(1.00)
Del Peak 29(13q12 11) 145 (45%) 177 8.03e-11
(4.46e-08) 		7.28e-07
(0.000377) 		0.594
(1.00) 		0.474
(1.00) 		0.053
(1.00) 		0.0289
(1.00) 		0.693
(1.00) 		0.319
(1.00)
Del Peak 37(18q21 2) 170 (53%) 152 3.21e-14
(1.82e-11) 		1.69e-09
(9.24e-07) 		0.497
(1.00) 		0.495
(1.00) 		0.00268
(1.00) 		0.0073
(1.00) 		0.0133
(1.00) 		0.0318
(1.00)
Del Peak 38(18q23) 182 (57%) 140 2.42e-16
(1.38e-13) 		1.38e-11
(7.7e-09) 		0.136
(1.00) 		0.217
(1.00) 		0.00216
(0.972) 		0.00333
(1.00) 		0.0151
(1.00) 		0.0359
(1.00)
Del Peak 40(19q13 43) 64 (20%) 258 9.26e-05
(0.0454) 		6.93e-05
(0.0342) 		0.671
(1.00) 		0.138
(1.00) 		0.584
(1.00) 		0.262
(1.00) 		0.0578
(1.00) 		0.774
(1.00)
Del Peak 42(Xp11 3) 108 (34%) 214 9.69e-08
(5.15e-05) 		5.8e-05
(0.0288) 		0.139
(1.00) 		0.005
(1.00) 		0.211
(1.00) 		0.0598
(1.00) 		0.176
(1.00) 		0.21
(1.00)
Del Peak 43(Xq21 33) 55 (17%) 267 1.07e-06
(0.000548) 		0.00166
(0.752) 		0.0322
(1.00) 		0.701
(1.00) 		0.00131
(0.594) 		0.0123
(1.00) 		0.000324
(0.154) 		0.00524
(1.00)
Amp Peak 6(5p15 33) 147 (46%) 175 9.05e-11
(5.02e-08) 		0.0256
(1.00) 		0.437
(1.00) 		0.513
(1.00) 		0.683
(1.00) 		0.32
(1.00) 		0.665
(1.00) 		0.179
(1.00)
Amp Peak 7(5p12) 122 (38%) 200 1.83e-10
(1.01e-07) 		0.0182
(1.00) 		0.823
(1.00) 		0.86
(1.00) 		0.9
(1.00) 		0.388
(1.00) 		0.819
(1.00) 		0.676
(1.00)
Amp Peak 8(6p12 1) 64 (20%) 258 1.65e-05
(0.00829) 		0.0028
(1.00) 		0.952
(1.00) 		0.676
(1.00) 		0.983
(1.00) 		0.802
(1.00) 		0.744
(1.00) 		0.666
(1.00)
Amp Peak 13(8q11 21) 189 (59%) 133 1.02e-06
(0.000525) 		0.0111
(1.00) 		0.902
(1.00) 		0.764
(1.00) 		0.00113
(0.515) 		0.000664
(0.31) 		0.0666
(1.00) 		0.0023
(1.00)
Amp Peak 19(11q13 3) 146 (45%) 176 1.04e-23
(5.94e-21) 		0.000897
(0.412) 		0.904
(1.00) 		0.263
(1.00) 		0.361
(1.00) 		0.504
(1.00) 		0.723
(1.00) 		0.81
(1.00)
Amp Peak 21(12q15) 63 (20%) 259 3.77e-08
(2.03e-05) 		0.00842
(1.00) 		0.425
(1.00) 		0.0996
(1.00) 		0.09
(1.00) 		0.0459
(1.00) 		0.486
(1.00) 		0.666
(1.00)
Amp Peak 23(14q11 2) 88 (27%) 234 7.37e-06
(0.00375) 		0.0239
(1.00) 		0.636
(1.00) 		0.845
(1.00) 		0.053
(1.00) 		0.384
(1.00) 		0.00616
(1.00) 		0.126
(1.00)
Amp Peak 24(15q26 3) 71 (22%) 251 0.000106
(0.0517) 		0.217
(1.00) 		0.504
(1.00) 		0.932
(1.00) 		0.923
(1.00) 		0.416
(1.00) 		0.44
(1.00) 		0.265
(1.00)
Amp Peak 26(18p11 31) 103 (32%) 219 4.38e-07
(0.000229) 		0.00306
(1.00) 		0.873
(1.00) 		0.735
(1.00) 		0.238
(1.00) 		0.169
(1.00) 		0.759
(1.00) 		0.73
(1.00)
Amp Peak 28(20q11 22) 145 (45%) 177 0.000225
(0.108) 		0.0222
(1.00) 		0.436
(1.00) 		0.559
(1.00) 		0.0128
(1.00) 		0.0854
(1.00) 		0.715
(1.00) 		0.0965
(1.00)
Amp Peak 29(Xq28) 98 (30%) 224 3.96e-08
(2.13e-05) 		0.0032
(1.00) 		0.561
(1.00) 		0.578
(1.00) 		0.188
(1.00) 		0.463
(1.00) 		0.338
(1.00) 		0.209
(1.00)
Del Peak 4(2q22 1) 66 (20%) 256 0.0906
(1.00) 		0.00648
(1.00) 		0.855
(1.00) 		0.338
(1.00) 		0.0513
(1.00) 		0.0292
(1.00) 		0.0954
(1.00) 		0.000186
(0.0894)
Del Peak 15(6p25 3) 64 (20%) 258 0.00338
(1.00) 		0.00033
(0.156) 		0.0346
(1.00) 		0.0862
(1.00) 		0.00752
(1.00) 		0.38
(1.00) 		0.0054
(1.00) 		0.625
(1.00)
Del Peak 21(9q21 11) 61 (19%) 261 2.24e-07
(0.000118) 		0.000962
(0.441) 		0.574
(1.00) 		0.821
(1.00) 		0.882
(1.00) 		0.673
(1.00) 		0.831
(1.00) 		0.0214
(1.00)
Del Peak 23(10p15 3) 108 (34%) 214 1.84e-05
(0.00926) 		0.0293
(1.00) 		0.929
(1.00) 		0.218
(1.00) 		0.327
(1.00) 		0.307
(1.00) 		0.621
(1.00) 		0.473
(1.00)
Del Peak 24(10p11 21) 101 (31%) 221 8.15e-06
(0.00413) 		0.145
(1.00) 		0.603
(1.00) 		0.0924
(1.00) 		0.702
(1.00) 		0.975
(1.00) 		0.942
(1.00) 		0.67
(1.00)
Del Peak 35(16q23 3) 64 (20%) 258 0.074
(1.00) 		0.000839
(0.386) 		0.133
(1.00) 		0.0394
(1.00) 		0.000601
(0.282) 		8.88e-05
(0.0437) 		0.0333
(1.00) 		0.0641
(1.00)
Del Peak 41(Xp21 3) 106 (33%) 216 7.73e-06
(0.00393) 		0.00532
(1.00) 		0.139
(1.00) 		0.0371
(1.00) 		0.275
(1.00) 		0.0415
(1.00) 		0.121
(1.00) 		0.834
(1.00)
Amp Peak 9(6q12) 59 (18%) 263 0.000695
(0.323) 		0.0138
(1.00) 		0.878
(1.00) 		0.527
(1.00) 		1
(1.00) 		0.822
(1.00) 		0.705
(1.00) 		0.929
(1.00)
Amp Peak 12(8p11 23) 102 (32%) 220 0.0409
(1.00) 		0.0369
(1.00) 		0.673
(1.00) 		0.413
(1.00) 		0.15
(1.00) 		0.0182
(1.00) 		0.0121
(1.00) 		0.00753
(1.00)
Amp Peak 15(9p23) 76 (24%) 246 0.00248
(1.00) 		0.786
(1.00) 		1
(1.00) 		0.647
(1.00) 		0.0993
(1.00) 		0.227
(1.00) 		0.438
(1.00) 		0.728
(1.00)
Amp Peak 16(9p13 3) 90 (28%) 232 0.00223
(0.999) 		0.222
(1.00) 		0.587
(1.00) 		0.165
(1.00) 		0.00708
(1.00) 		0.0379
(1.00) 		0.107
(1.00) 		0.0574
(1.00)
Amp Peak 17(11p13) 63 (20%) 259 0.0177
(1.00) 		0.0971
(1.00) 		0.343
(1.00) 		0.033
(1.00) 		0.631
(1.00) 		0.163
(1.00) 		0.682
(1.00) 		0.965
(1.00)
Amp Peak 18(11p11 2) 63 (20%) 259 0.14
(1.00) 		0.533
(1.00) 		0.203
(1.00) 		0.336
(1.00) 		0.626
(1.00) 		0.148
(1.00) 		0.671
(1.00) 		0.339
(1.00)
Amp Peak 27(18q11 2) 71 (22%) 251 0.0131
(1.00) 		0.033
(1.00) 		0.468
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.689
(1.00) 		0.49
(1.00) 		0.451
(1.00)
Del Peak 3(2q21 2) 40 (12%) 282 0.289
(1.00) 		0.0278
(1.00) 		0.734
(1.00) 		0.947
(1.00) 		0.0154
(1.00) 		0.00564
(1.00) 		0.00349
(1.00) 		0.093
(1.00)
Del Peak 16(7q31 1) 49 (15%) 273 0.00197
(0.887) 		0.0261
(1.00) 		0.563
(1.00) 		0.624
(1.00) 		0.363
(1.00) 		0.609
(1.00) 		0.167
(1.00) 		0.279
(1.00)
Del Peak 17(7q36 1) 80 (25%) 242 0.0292
(1.00) 		0.33
(1.00) 		0.251
(1.00) 		0.367
(1.00) 		0.957
(1.00) 		0.674
(1.00) 		0.339
(1.00) 		0.0237
(1.00)
Del Peak 22(9q34 3) 53 (16%) 269 0.000667
(0.311) 		0.0316
(1.00) 		0.374
(1.00) 		0.116
(1.00) 		0.851
(1.00) 		0.409
(1.00) 		0.473
(1.00) 		0.278
(1.00)
Del Peak 25(10q23 31) 83 (26%) 239 0.00454
(1.00) 		0.00416
(1.00) 		0.865
(1.00) 		0.699
(1.00) 		0.0249
(1.00) 		0.0128
(1.00) 		0.276
(1.00) 		0.761
(1.00)
Del Peak 28(12q24 33) 38 (12%) 284 0.0127
(1.00) 		0.0646
(1.00) 		0.0245
(1.00) 		0.57
(1.00) 		0.859
(1.00) 		0.775
(1.00) 		0.492
(1.00) 		0.11
(1.00)
Del Peak 31(14q11 2) 46 (14%) 276 0.0264
(1.00) 		0.00616
(1.00) 		0.519
(1.00) 		0.317
(1.00) 		0.463
(1.00) 		0.329
(1.00) 		0.0897
(1.00) 		0.0487
(1.00)
Del Peak 33(15q15 1) 76 (24%) 246 0.00392
(1.00) 		0.501
(1.00) 		0.381
(1.00) 		0.137
(1.00) 		0.0233
(1.00) 		0.0488
(1.00) 		0.367
(1.00) 		0.255
(1.00)
Del Peak 36(17q25 3) 41 (13%) 281 0.0479
(1.00) 		0.123
(1.00) 		0.128
(1.00) 		0.875
(1.00) 		0.037
(1.00) 		0.0612
(1.00) 		0.0072
(1.00) 		0.0403
(1.00)
Del Peak 39(19p13 3) 110 (34%) 212 0.00186
(0.843) 		0.0368
(1.00) 		0.852
(1.00) 		0.0758
(1.00) 		0.0876
(1.00) 		0.761
(1.00) 		0.758
(1.00) 		0.774
(1.00)
'Amp Peak 1(1q21.2) mutation analysis' versus 'CN_CNMF'

P value = 1.21e-07 (Chi-square test), Q value = 6.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 1(1Q21.2) MUTATED 26 12 21 10 2 3 2
AMP PEAK 1(1Q21.2) WILD-TYPE 40 29 25 75 20 7 50

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 2.63e-08 (Chi-square test), Q value = 1.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 1(1Q21.2) MUTATED 8 13 4 10 31 1 0 4
AMP PEAK 1(1Q21.2) WILD-TYPE 35 34 35 35 27 50 4 15

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

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

P value = 0.000509 (Fisher's exact test), Q value = 0.24

Table S3.  Gene #1: 'Amp Peak 1(1q21.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
AMP PEAK 1(1Q21.2) MUTATED 41 16 12
AMP PEAK 1(1Q21.2) WILD-TYPE 77 75 78

Figure S3.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

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

P value = 0.000103 (Fisher's exact test), Q value = 0.05

Table S4.  Gene #1: 'Amp Peak 1(1q21.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 127 93
AMP PEAK 1(1Q21.2) MUTATED 11 44 21
AMP PEAK 1(1Q21.2) WILD-TYPE 90 83 72

Figure S4.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

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

P value = 3.48e-06 (Chi-square test), Q value = 0.0018

Table S5.  Gene #2: 'Amp Peak 2(2q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 2(2Q11.2) MUTATED 19 14 20 5 4 1 6
AMP PEAK 2(2Q11.2) WILD-TYPE 47 27 26 80 18 9 46

Figure S5.  Get High-res Image Gene #2: 'Amp Peak 2(2q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 2(2q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.71e-08 (Chi-square test), Q value = 9.3e-06

Table S6.  Gene #2: 'Amp Peak 2(2q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 2(2Q11.2) MUTATED 19 9 4 1 26 5 1 2
AMP PEAK 2(2Q11.2) WILD-TYPE 24 38 35 44 32 46 3 17

Figure S6.  Get High-res Image Gene #2: 'Amp Peak 2(2q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 8.38e-10 (Chi-square test), Q value = 4.6e-07

Table S7.  Gene #3: 'Amp Peak 3(2q31.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 3(2Q31.2) MUTATED 23 15 20 3 2 0 4
AMP PEAK 3(2Q31.2) WILD-TYPE 43 26 26 82 20 10 48

Figure S7.  Get High-res Image Gene #3: 'Amp Peak 3(2q31.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 9.37e-09 (Chi-square test), Q value = 5.1e-06

Table S8.  Gene #3: 'Amp Peak 3(2q31.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 3(2Q31.2) MUTATED 13 8 5 2 30 5 1 1
AMP PEAK 3(2Q31.2) WILD-TYPE 30 39 34 43 28 46 3 18

Figure S8.  Get High-res Image Gene #3: 'Amp Peak 3(2q31.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 4(2q32.2) mutation analysis' versus 'CN_CNMF'

P value = 7.97e-07 (Chi-square test), Q value = 0.00041

Table S9.  Gene #4: 'Amp Peak 4(2q32.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 4(2Q32.2) MUTATED 20 13 16 2 3 1 4
AMP PEAK 4(2Q32.2) WILD-TYPE 46 28 30 83 19 9 48

Figure S9.  Get High-res Image Gene #4: 'Amp Peak 4(2q32.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 4(2q32.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.3e-08 (Chi-square test), Q value = 2.8e-05

Table S10.  Gene #4: 'Amp Peak 4(2q32.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 4(2Q32.2) MUTATED 13 4 5 2 26 3 1 2
AMP PEAK 4(2Q32.2) WILD-TYPE 30 43 34 43 32 48 3 17

Figure S10.  Get High-res Image Gene #4: 'Amp Peak 4(2q32.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 1.29e-09 (Chi-square test), Q value = 7.1e-07

Table S11.  Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 5(3Q26.33) MUTATED 54 35 46 41 18 8 40
AMP PEAK 5(3Q26.33) WILD-TYPE 12 6 0 44 4 2 12

Figure S11.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 3.26e-05 (Chi-square test), Q value = 0.016

Table S12.  Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 5(3Q26.33) MUTATED 34 38 25 36 55 30 2 9
AMP PEAK 5(3Q26.33) WILD-TYPE 9 9 14 9 3 21 2 10

Figure S12.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 0.000288 (Fisher's exact test), Q value = 0.14

Table S13.  Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
AMP PEAK 5(3Q26.33) MUTATED 75 50 101
AMP PEAK 5(3Q26.33) WILD-TYPE 20 34 19

Figure S13.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(5p15.33) mutation analysis' versus 'CN_CNMF'

P value = 9.05e-11 (Chi-square test), Q value = 5e-08

Table S14.  Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 6(5P15.33) MUTATED 37 27 22 25 22 3 11
AMP PEAK 6(5P15.33) WILD-TYPE 29 14 24 60 0 7 41

Figure S14.  Get High-res Image Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 7(5p12) mutation analysis' versus 'CN_CNMF'

P value = 1.83e-10 (Chi-square test), Q value = 1e-07

Table S15.  Gene #7: 'Amp Peak 7(5p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 7(5P12) MUTATED 26 21 21 17 22 2 13
AMP PEAK 7(5P12) WILD-TYPE 40 20 25 68 0 8 39

Figure S15.  Get High-res Image Gene #7: 'Amp Peak 7(5p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 8(6p12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.65e-05 (Chi-square test), Q value = 0.0083

Table S16.  Gene #8: 'Amp Peak 8(6p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 8(6P12.1) MUTATED 19 18 10 6 5 2 4
AMP PEAK 8(6P12.1) WILD-TYPE 47 23 36 79 17 8 48

Figure S16.  Get High-res Image Gene #8: 'Amp Peak 8(6p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 10(7p11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.91e-08 (Chi-square test), Q value = 1e-05

Table S17.  Gene #10: 'Amp Peak 10(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 10(7P11.2) MUTATED 36 32 22 20 11 1 15
AMP PEAK 10(7P11.2) WILD-TYPE 30 9 24 65 11 9 37

Figure S17.  Get High-res Image Gene #10: 'Amp Peak 10(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 10(7p11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.87e-07 (Chi-square test), Q value = 0.00036

Table S18.  Gene #10: 'Amp Peak 10(7p11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 10(7P11.2) MUTATED 27 24 21 3 31 15 1 9
AMP PEAK 10(7P11.2) WILD-TYPE 16 23 18 42 27 36 3 10

Figure S18.  Get High-res Image Gene #10: 'Amp Peak 10(7p11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 11(7q22.1) mutation analysis' versus 'CN_CNMF'

P value = 3.1e-11 (Chi-square test), Q value = 1.7e-08

Table S19.  Gene #11: 'Amp Peak 11(7q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 11(7Q22.1) MUTATED 42 17 25 13 9 0 8
AMP PEAK 11(7Q22.1) WILD-TYPE 24 24 21 72 13 10 44

Figure S19.  Get High-res Image Gene #11: 'Amp Peak 11(7q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 11(7q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.46e-08 (Chi-square test), Q value = 2.9e-05

Table S20.  Gene #11: 'Amp Peak 11(7q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 11(7Q22.1) MUTATED 16 11 15 6 40 11 2 5
AMP PEAK 11(7Q22.1) WILD-TYPE 27 36 24 39 18 40 2 14

Figure S20.  Get High-res Image Gene #11: 'Amp Peak 11(7q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 13(8q11.21) mutation analysis' versus 'CN_CNMF'

P value = 1.02e-06 (Chi-square test), Q value = 0.00052

Table S21.  Gene #13: 'Amp Peak 13(8q11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 13(8Q11.21) MUTATED 43 34 17 35 16 9 35
AMP PEAK 13(8Q11.21) WILD-TYPE 23 7 29 50 6 1 17

Figure S21.  Get High-res Image Gene #13: 'Amp Peak 13(8q11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 14(8q24.21) mutation analysis' versus 'CN_CNMF'

P value = 5.76e-08 (Chi-square test), Q value = 3.1e-05

Table S22.  Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 14(8Q24.21) MUTATED 59 36 28 42 18 10 39
AMP PEAK 14(8Q24.21) WILD-TYPE 7 5 18 43 4 0 13

Figure S22.  Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 14(8q24.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000106 (Chi-square test), Q value = 0.052

Table S23.  Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 14(8Q24.21) MUTATED 30 42 32 20 40 33 4 16
AMP PEAK 14(8Q24.21) WILD-TYPE 13 5 7 25 18 18 0 3

Figure S23.  Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 14(8q24.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.05

Table S24.  Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
AMP PEAK 14(8Q24.21) MUTATED 69 77 68
AMP PEAK 14(8Q24.21) WILD-TYPE 49 14 22

Figure S24.  Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Amp Peak 14(8q24.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000135 (Fisher's exact test), Q value = 0.065

Table S25.  Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
AMP PEAK 14(8Q24.21) MUTATED 79 65 70
AMP PEAK 14(8Q24.21) WILD-TYPE 16 19 50

Figure S25.  Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(8q24.21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000169 (Fisher's exact test), Q value = 0.082

Table S26.  Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 130 10
AMP PEAK 14(8Q24.21) MUTATED 114 109 8
AMP PEAK 14(8Q24.21) WILD-TYPE 67 21 2

Figure S26.  Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 19(11q13.3) mutation analysis' versus 'CN_CNMF'

P value = 1.04e-23 (Chi-square test), Q value = 5.9e-21

Table S27.  Gene #19: 'Amp Peak 19(11q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 19(11Q13.3) MUTATED 66 17 22 11 10 2 18
AMP PEAK 19(11Q13.3) WILD-TYPE 0 24 24 74 12 8 34

Figure S27.  Get High-res Image Gene #19: 'Amp Peak 19(11q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 20(12p13.33) mutation analysis' versus 'CN_CNMF'

P value = 5.52e-11 (Chi-square test), Q value = 3.1e-08

Table S28.  Gene #20: 'Amp Peak 20(12p13.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 20(12P13.33) MUTATED 24 25 28 12 10 5 5
AMP PEAK 20(12P13.33) WILD-TYPE 42 16 18 73 12 5 47

Figure S28.  Get High-res Image Gene #20: 'Amp Peak 20(12p13.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 20(12p13.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.28e-05 (Chi-square test), Q value = 0.0065

Table S29.  Gene #20: 'Amp Peak 20(12p13.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 20(12P13.33) MUTATED 20 20 5 14 34 12 0 3
AMP PEAK 20(12P13.33) WILD-TYPE 23 27 34 31 24 39 4 16

Figure S29.  Get High-res Image Gene #20: 'Amp Peak 20(12p13.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 21(12q15) mutation analysis' versus 'CN_CNMF'

P value = 3.77e-08 (Chi-square test), Q value = 2e-05

Table S30.  Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 21(12Q15) MUTATED 20 20 9 7 3 3 1
AMP PEAK 21(12Q15) WILD-TYPE 46 21 37 78 19 7 51

Figure S30.  Get High-res Image Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 22(13q22.1) mutation analysis' versus 'CN_CNMF'

P value = 4.16e-07 (Chi-square test), Q value = 0.00022

Table S31.  Gene #22: 'Amp Peak 22(13q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 22(13Q22.1) MUTATED 19 21 3 7 3 2 13
AMP PEAK 22(13Q22.1) WILD-TYPE 47 20 43 78 19 8 39

Figure S31.  Get High-res Image Gene #22: 'Amp Peak 22(13q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 22(13q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.43e-05 (Chi-square test), Q value = 0.042

Table S32.  Gene #22: 'Amp Peak 22(13q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 22(13Q22.1) MUTATED 7 23 7 10 12 3 0 5
AMP PEAK 22(13Q22.1) WILD-TYPE 36 24 32 35 46 48 4 14

Figure S32.  Get High-res Image Gene #22: 'Amp Peak 22(13q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 23(14q11.2) mutation analysis' versus 'CN_CNMF'

P value = 7.37e-06 (Chi-square test), Q value = 0.0038

Table S33.  Gene #23: 'Amp Peak 23(14q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 23(14Q11.2) MUTATED 20 23 15 8 7 4 11
AMP PEAK 23(14Q11.2) WILD-TYPE 46 18 31 77 15 6 41

Figure S33.  Get High-res Image Gene #23: 'Amp Peak 23(14q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 24(15q26.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000106 (Chi-square test), Q value = 0.052

Table S34.  Gene #24: 'Amp Peak 24(15q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 24(15Q26.3) MUTATED 24 17 9 9 5 1 6
AMP PEAK 24(15Q26.3) WILD-TYPE 42 24 37 76 17 9 46

Figure S34.  Get High-res Image Gene #24: 'Amp Peak 24(15q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 25(17q12) mutation analysis' versus 'CN_CNMF'

P value = 4.94e-05 (Chi-square test), Q value = 0.025

Table S35.  Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 25(17Q12) MUTATED 21 10 12 3 3 3 4
AMP PEAK 25(17Q12) WILD-TYPE 45 31 34 82 19 7 48

Figure S35.  Get High-res Image Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 25(17q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000112 (Chi-square test), Q value = 0.054

Table S36.  Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
AMP PEAK 25(17Q12) MUTATED 10 8 2 4 22 4 0 2
AMP PEAK 25(17Q12) WILD-TYPE 33 39 37 41 36 47 4 17

Figure S36.  Get High-res Image Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 26(18p11.31) mutation analysis' versus 'CN_CNMF'

P value = 4.38e-07 (Chi-square test), Q value = 0.00023

Table S37.  Gene #26: 'Amp Peak 26(18p11.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 26(18P11.31) MUTATED 26 18 21 11 13 6 8
AMP PEAK 26(18P11.31) WILD-TYPE 40 23 25 74 9 4 44

Figure S37.  Get High-res Image Gene #26: 'Amp Peak 26(18p11.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 28(20q11.22) mutation analysis' versus 'CN_CNMF'

P value = 0.000225 (Chi-square test), Q value = 0.11

Table S38.  Gene #28: 'Amp Peak 28(20q11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 28(20Q11.22) MUTATED 30 31 19 27 13 6 19
AMP PEAK 28(20Q11.22) WILD-TYPE 36 10 27 58 9 4 33

Figure S38.  Get High-res Image Gene #28: 'Amp Peak 28(20q11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 29(Xq28) mutation analysis' versus 'CN_CNMF'

P value = 3.96e-08 (Chi-square test), Q value = 2.1e-05

Table S39.  Gene #29: 'Amp Peak 29(Xq28) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
AMP PEAK 29(XQ28) MUTATED 31 23 9 12 9 6 8
AMP PEAK 29(XQ28) WILD-TYPE 35 18 37 73 13 4 44

Figure S39.  Get High-res Image Gene #29: 'Amp Peak 29(Xq28) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p36.13) mutation analysis' versus 'CN_CNMF'

P value = 1.48e-10 (Chi-square test), Q value = 8.2e-08

Table S40.  Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 1(1P36.13) MUTATED 14 14 26 10 0 0 4
DEL PEAK 1(1P36.13) WILD-TYPE 52 27 20 75 22 10 48

Figure S40.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p36.13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.38e-15 (Chi-square test), Q value = 3.1e-12

Table S41.  Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 1(1P36.13) MUTATED 6 4 8 5 36 1 2 2
DEL PEAK 1(1P36.13) WILD-TYPE 37 43 31 40 22 50 2 17

Figure S41.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 1(1p36.13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.015

Table S42.  Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
DEL PEAK 1(1P36.13) MUTATED 39 17 7
DEL PEAK 1(1P36.13) WILD-TYPE 79 74 83

Figure S42.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

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

P value = 2.77e-10 (Chi-square test), Q value = 1.5e-07

Table S43.  Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 2(1P13.2) MUTATED 16 16 28 5 6 3 7
DEL PEAK 2(1P13.2) WILD-TYPE 50 25 18 80 16 7 45

Figure S43.  Get High-res Image Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 8.62e-10 (Chi-square test), Q value = 4.7e-07

Table S44.  Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 2(1P13.2) MUTATED 10 9 6 4 35 5 2 4
DEL PEAK 2(1P13.2) WILD-TYPE 33 38 33 41 23 46 2 15

Figure S44.  Get High-res Image Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 0.000181 (Fisher's exact test), Q value = 0.087

Table S45.  Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 127 93
DEL PEAK 2(1P13.2) MUTATED 16 48 17
DEL PEAK 2(1P13.2) WILD-TYPE 85 79 76

Figure S45.  Get High-res Image Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

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

P value = 0.000186 (Fisher's exact test), Q value = 0.089

Table S46.  Gene #33: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 130 10
DEL PEAK 4(2Q22.1) MUTATED 45 15 6
DEL PEAK 4(2Q22.1) WILD-TYPE 136 115 4

Figure S46.  Get High-res Image Gene #33: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000122 (Chi-square test), Q value = 0.059

Table S47.  Gene #34: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 5(2Q36.2) MUTATED 21 14 27 15 4 3 12
DEL PEAK 5(2Q36.2) WILD-TYPE 45 27 19 70 18 7 40

Figure S47.  Get High-res Image Gene #34: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 5.69e-06 (Chi-square test), Q value = 0.0029

Table S48.  Gene #34: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 5(2Q36.2) MUTATED 14 11 16 15 29 2 3 3
DEL PEAK 5(2Q36.2) WILD-TYPE 29 36 23 30 29 49 1 16

Figure S48.  Get High-res Image Gene #34: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 6(3p24.1) mutation analysis' versus 'CN_CNMF'

P value = 3.25e-27 (Chi-square test), Q value = 1.9e-24

Table S49.  Gene #35: 'Del Peak 6(3p24.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 6(3P24.1) MUTATED 62 34 42 23 22 8 48
DEL PEAK 6(3P24.1) WILD-TYPE 4 7 4 62 0 2 4

Figure S49.  Get High-res Image Gene #35: 'Del Peak 6(3p24.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 6(3p24.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.93e-08 (Chi-square test), Q value = 2.1e-05

Table S50.  Gene #35: 'Del Peak 6(3p24.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 6(3P24.1) MUTATED 39 42 28 20 51 29 4 14
DEL PEAK 6(3P24.1) WILD-TYPE 4 5 11 25 7 22 0 5

Figure S50.  Get High-res Image Gene #35: 'Del Peak 6(3p24.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'CN_CNMF'

P value = 3.41e-27 (Chi-square test), Q value = 2e-24

Table S51.  Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 7(3P14.2) MUTATED 62 35 43 24 21 9 48
DEL PEAK 7(3P14.2) WILD-TYPE 4 6 3 61 1 1 4

Figure S51.  Get High-res Image Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.71e-07 (Chi-square test), Q value = 3e-04

Table S52.  Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 7(3P14.2) MUTATED 41 41 27 23 51 30 4 14
DEL PEAK 7(3P14.2) WILD-TYPE 2 6 12 22 7 21 0 5

Figure S52.  Get High-res Image Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 8(3p12.2) mutation analysis' versus 'CN_CNMF'

P value = 3.11e-25 (Chi-square test), Q value = 1.8e-22

Table S53.  Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 8(3P12.2) MUTATED 59 34 44 20 20 9 42
DEL PEAK 8(3P12.2) WILD-TYPE 7 7 2 65 2 1 10

Figure S53.  Get High-res Image Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 8(3p12.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.04e-09 (Chi-square test), Q value = 2.2e-06

Table S54.  Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 8(3P12.2) MUTATED 38 38 27 18 53 26 4 13
DEL PEAK 8(3P12.2) WILD-TYPE 5 9 12 27 5 25 0 6

Figure S54.  Get High-res Image Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 9(4p16.3) mutation analysis' versus 'CN_CNMF'

P value = 1.38e-14 (Chi-square test), Q value = 7.8e-12

Table S55.  Gene #38: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 9(4P16.3) MUTATED 44 25 34 13 4 2 15
DEL PEAK 9(4P16.3) WILD-TYPE 22 16 12 72 18 8 37

Figure S55.  Get High-res Image Gene #38: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(4p16.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.5e-05 (Chi-square test), Q value = 0.0076

Table S56.  Gene #38: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 9(4P16.3) MUTATED 20 17 17 13 41 11 3 9
DEL PEAK 9(4P16.3) WILD-TYPE 23 30 22 32 17 40 1 10

Figure S56.  Get High-res Image Gene #38: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 7.36e-16 (Chi-square test), Q value = 4.2e-13

Table S57.  Gene #39: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 10(4P15.2) MUTATED 41 25 38 13 4 2 15
DEL PEAK 10(4P15.2) WILD-TYPE 25 16 8 72 18 8 37

Figure S57.  Get High-res Image Gene #39: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 5.98e-07 (Chi-square test), Q value = 0.00031

Table S58.  Gene #39: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 10(4P15.2) MUTATED 20 15 17 13 44 12 3 7
DEL PEAK 10(4P15.2) WILD-TYPE 23 32 22 32 14 39 1 12

Figure S58.  Get High-res Image Gene #39: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 5.42e-12 (Chi-square test), Q value = 3e-09

Table S59.  Gene #40: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 11(4Q22.1) MUTATED 21 24 30 9 9 2 7
DEL PEAK 11(4Q22.1) WILD-TYPE 45 17 16 76 13 8 45

Figure S59.  Get High-res Image Gene #40: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 6.5e-07 (Chi-square test), Q value = 0.00034

Table S60.  Gene #40: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 11(4Q22.1) MUTATED 17 16 11 7 36 8 1 2
DEL PEAK 11(4Q22.1) WILD-TYPE 26 31 28 38 22 43 3 17

Figure S60.  Get High-res Image Gene #40: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 4e-08 (Chi-square test), Q value = 2.1e-05

Table S61.  Gene #41: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 12(4Q35.2) MUTATED 21 28 29 17 14 3 19
DEL PEAK 12(4Q35.2) WILD-TYPE 45 13 17 68 8 7 33

Figure S61.  Get High-res Image Gene #41: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 2.97e-05 (Chi-square test), Q value = 0.015

Table S62.  Gene #41: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 12(4Q35.2) MUTATED 17 25 19 9 36 12 0 6
DEL PEAK 12(4Q35.2) WILD-TYPE 26 22 20 36 22 39 4 13

Figure S62.  Get High-res Image Gene #41: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 1.65e-16 (Chi-square test), Q value = 9.5e-14

Table S63.  Gene #42: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 13(5Q11.2) MUTATED 32 32 33 8 13 2 14
DEL PEAK 13(5Q11.2) WILD-TYPE 34 9 13 77 9 8 38

Figure S63.  Get High-res Image Gene #42: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 1.35e-12 (Chi-square test), Q value = 7.6e-10

Table S64.  Gene #42: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 13(5Q11.2) MUTATED 30 27 8 6 41 11 1 6
DEL PEAK 13(5Q11.2) WILD-TYPE 13 20 31 39 17 40 3 13

Figure S64.  Get High-res Image Gene #42: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 14(5q35.3) mutation analysis' versus 'CN_CNMF'

P value = 4.01e-15 (Chi-square test), Q value = 2.3e-12

Table S65.  Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 14(5Q35.3) MUTATED 26 29 34 10 14 2 12
DEL PEAK 14(5Q35.3) WILD-TYPE 40 12 12 75 8 8 40

Figure S65.  Get High-res Image Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(5q35.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.25e-14 (Chi-square test), Q value = 2.4e-11

Table S66.  Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 14(5Q35.3) MUTATED 33 24 5 8 37 8 0 6
DEL PEAK 14(5Q35.3) WILD-TYPE 10 23 34 37 21 43 4 13

Figure S66.  Get High-res Image Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 14(5q35.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000477 (Fisher's exact test), Q value = 0.23

Table S67.  Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 14(5Q35.3) MUTATED 39 20 61
DEL PEAK 14(5Q35.3) WILD-TYPE 56 64 59

Figure S67.  Get High-res Image Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.00033 (Chi-square test), Q value = 0.16

Table S68.  Gene #44: 'Del Peak 15(6p25.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 15(6P25.3) MUTATED 7 9 5 6 26 6 1 3
DEL PEAK 15(6P25.3) WILD-TYPE 36 38 34 39 32 45 3 16

Figure S68.  Get High-res Image Gene #44: 'Del Peak 15(6p25.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 18(8p23.2) mutation analysis' versus 'CN_CNMF'

P value = 4.99e-12 (Chi-square test), Q value = 2.8e-09

Table S69.  Gene #47: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 18(8P23.2) MUTATED 54 31 17 24 17 5 35
DEL PEAK 18(8P23.2) WILD-TYPE 12 10 29 61 5 5 17

Figure S69.  Get High-res Image Gene #47: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 18(8p23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.84e-05 (Chi-square test), Q value = 0.019

Table S70.  Gene #47: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 18(8P23.2) MUTATED 21 34 30 11 36 28 2 11
DEL PEAK 18(8P23.2) WILD-TYPE 22 13 9 34 22 23 2 8

Figure S70.  Get High-res Image Gene #47: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 19(9p23) mutation analysis' versus 'CN_CNMF'

P value = 6.45e-13 (Chi-square test), Q value = 3.6e-10

Table S71.  Gene #48: 'Del Peak 19(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 19(9P23) MUTATED 40 27 27 11 15 0 31
DEL PEAK 19(9P23) WILD-TYPE 26 14 19 74 7 10 21

Figure S71.  Get High-res Image Gene #48: 'Del Peak 19(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 19(9p23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.42e-09 (Chi-square test), Q value = 2.9e-06

Table S72.  Gene #48: 'Del Peak 19(9p23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 19(9P23) MUTATED 30 25 20 5 38 13 3 8
DEL PEAK 19(9P23) WILD-TYPE 13 22 19 40 20 38 1 11

Figure S72.  Get High-res Image Gene #48: 'Del Peak 19(9p23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 20(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 3.52e-10 (Chi-square test), Q value = 1.9e-07

Table S73.  Gene #49: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 20(9P21.3) MUTATED 53 25 31 25 16 2 37
DEL PEAK 20(9P21.3) WILD-TYPE 13 16 15 60 6 8 15

Figure S73.  Get High-res Image Gene #49: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 20(9p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.83e-09 (Chi-square test), Q value = 1.5e-06

Table S74.  Gene #49: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 20(9P21.3) MUTATED 35 30 26 7 40 23 3 14
DEL PEAK 20(9P21.3) WILD-TYPE 8 17 13 38 18 28 1 5

Figure S74.  Get High-res Image Gene #49: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 21(9q21.11) mutation analysis' versus 'CN_CNMF'

P value = 2.24e-07 (Chi-square test), Q value = 0.00012

Table S75.  Gene #50: 'Del Peak 21(9q21.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 21(9Q21.11) MUTATED 25 12 5 6 9 0 4
DEL PEAK 21(9Q21.11) WILD-TYPE 41 29 41 79 13 10 48

Figure S75.  Get High-res Image Gene #50: 'Del Peak 21(9q21.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 23(10p15.3) mutation analysis' versus 'CN_CNMF'

P value = 1.84e-05 (Chi-square test), Q value = 0.0093

Table S76.  Gene #52: 'Del Peak 23(10p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 23(10P15.3) MUTATED 28 20 15 9 8 6 22
DEL PEAK 23(10P15.3) WILD-TYPE 38 21 31 76 14 4 30

Figure S76.  Get High-res Image Gene #52: 'Del Peak 23(10p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 24(10p11.21) mutation analysis' versus 'CN_CNMF'

P value = 8.15e-06 (Chi-square test), Q value = 0.0041

Table S77.  Gene #53: 'Del Peak 24(10p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 24(10P11.21) MUTATED 28 22 11 9 8 5 18
DEL PEAK 24(10P11.21) WILD-TYPE 38 19 35 76 14 5 34

Figure S77.  Get High-res Image Gene #53: 'Del Peak 24(10p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(11p15.4) mutation analysis' versus 'CN_CNMF'

P value = 3.91e-06 (Chi-square test), Q value = 0.002

Table S78.  Gene #55: 'Del Peak 26(11p15.4) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 26(11P15.4) MUTATED 37 13 18 16 9 1 8
DEL PEAK 26(11P15.4) WILD-TYPE 29 28 28 69 13 9 44

Figure S78.  Get High-res Image Gene #55: 'Del Peak 26(11p15.4) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(11p15.4) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000523 (Chi-square test), Q value = 0.25

Table S79.  Gene #55: 'Del Peak 26(11p15.4) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 26(11P15.4) MUTATED 17 14 9 13 32 8 1 3
DEL PEAK 26(11P15.4) WILD-TYPE 26 33 30 32 26 43 3 16

Figure S79.  Get High-res Image Gene #55: 'Del Peak 26(11p15.4) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 27(11q23.1) mutation analysis' versus 'CN_CNMF'

P value = 1.37e-14 (Chi-square test), Q value = 7.8e-12

Table S80.  Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 27(11Q23.1) MUTATED 60 10 24 28 10 7 14
DEL PEAK 27(11Q23.1) WILD-TYPE 6 31 22 57 12 3 38

Figure S80.  Get High-res Image Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(11q23.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.45e-07 (Chi-square test), Q value = 0.00044

Table S81.  Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 27(11Q23.1) MUTATED 18 21 16 40 31 16 1 6
DEL PEAK 27(11Q23.1) WILD-TYPE 25 26 23 5 27 35 3 13

Figure S81.  Get High-res Image Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 27(11q23.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.11

Table S82.  Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 27(11Q23.1) MUTATED 37 33 76
DEL PEAK 27(11Q23.1) WILD-TYPE 58 51 44

Figure S82.  Get High-res Image Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(13q12.11) mutation analysis' versus 'CN_CNMF'

P value = 8.03e-11 (Chi-square test), Q value = 4.5e-08

Table S83.  Gene #58: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 29(13Q12.11) MUTATED 35 24 36 14 14 3 19
DEL PEAK 29(13Q12.11) WILD-TYPE 31 17 10 71 8 7 33

Figure S83.  Get High-res Image Gene #58: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 29(13q12.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.28e-07 (Chi-square test), Q value = 0.00038

Table S84.  Gene #58: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 29(13Q12.11) MUTATED 31 22 15 13 39 12 1 6
DEL PEAK 29(13Q12.11) WILD-TYPE 12 25 24 32 19 39 3 13

Figure S84.  Get High-res Image Gene #58: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 30(13q14.2) mutation analysis' versus 'CN_CNMF'

P value = 3.1e-07 (Chi-square test), Q value = 0.00016

Table S85.  Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 30(13Q14.2) MUTATED 32 18 35 22 13 4 13
DEL PEAK 30(13Q14.2) WILD-TYPE 34 23 11 63 9 6 39

Figure S85.  Get High-res Image Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 30(13q14.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.88e-07 (Chi-square test), Q value = 0.00031

Table S86.  Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 30(13Q14.2) MUTATED 32 17 13 23 31 10 0 4
DEL PEAK 30(13Q14.2) WILD-TYPE 11 30 26 22 27 41 4 15

Figure S86.  Get High-res Image Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 30(13q14.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.7e-05 (Fisher's exact test), Q value = 0.028

Table S87.  Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
DEL PEAK 30(13Q14.2) MUTATED 66 39 23
DEL PEAK 30(13Q14.2) WILD-TYPE 52 52 67

Figure S87.  Get High-res Image Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 30(13q14.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.46e-05 (Fisher's exact test), Q value = 0.032

Table S88.  Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 30(13Q14.2) MUTATED 38 22 68
DEL PEAK 30(13Q14.2) WILD-TYPE 57 62 52

Figure S88.  Get High-res Image Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(14q32.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.42e-07 (Chi-square test), Q value = 7.5e-05

Table S89.  Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 32(14Q32.32) MUTATED 5 3 4 20 13 1 0 1
DEL PEAK 32(14Q32.32) WILD-TYPE 38 44 35 25 45 50 4 18

Figure S89.  Get High-res Image Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 32(14q32.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.12

Table S90.  Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
DEL PEAK 32(14Q32.32) MUTATED 30 11 5
DEL PEAK 32(14Q32.32) WILD-TYPE 88 80 85

Figure S90.  Get High-res Image Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 32(14q32.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.048

Table S91.  Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 32(14Q32.32) MUTATED 11 4 31
DEL PEAK 32(14Q32.32) WILD-TYPE 84 80 89

Figure S91.  Get High-res Image Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(16q12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Chi-square test), Q value = 6e-05

Table S92.  Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 34(16Q12.1) MUTATED 8 1 5 21 13 2 1 1
DEL PEAK 34(16Q12.1) WILD-TYPE 35 46 34 24 45 49 3 18

Figure S92.  Get High-res Image Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 34(16q12.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.1e-08 (Fisher's exact test), Q value = 3.8e-05

Table S93.  Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 91 90
DEL PEAK 34(16Q12.1) MUTATED 38 9 4
DEL PEAK 34(16Q12.1) WILD-TYPE 80 82 86

Figure S93.  Get High-res Image Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 34(16q12.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.91e-07 (Fisher's exact test), Q value = 0.00021

Table S94.  Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 34(16Q12.1) MUTATED 7 6 38
DEL PEAK 34(16Q12.1) WILD-TYPE 88 78 82

Figure S94.  Get High-res Image Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(16q12.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.17

Table S95.  Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 127 93
DEL PEAK 34(16Q12.1) MUTATED 13 34 7
DEL PEAK 34(16Q12.1) WILD-TYPE 88 93 86

Figure S95.  Get High-res Image Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 35(16q23.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.88e-05 (Fisher's exact test), Q value = 0.044

Table S96.  Gene #64: 'Del Peak 35(16q23.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 84 120
DEL PEAK 35(16Q23.3) MUTATED 11 9 38
DEL PEAK 35(16Q23.3) WILD-TYPE 84 75 82

Figure S96.  Get High-res Image Gene #64: 'Del Peak 35(16q23.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(18q21.2) mutation analysis' versus 'CN_CNMF'

P value = 3.21e-14 (Chi-square test), Q value = 1.8e-11

Table S97.  Gene #66: 'Del Peak 37(18q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 37(18Q21.2) MUTATED 43 35 21 14 15 6 36
DEL PEAK 37(18Q21.2) WILD-TYPE 23 6 25 71 7 4 16

Figure S97.  Get High-res Image Gene #66: 'Del Peak 37(18q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 37(18q21.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.69e-09 (Chi-square test), Q value = 9.2e-07

Table S98.  Gene #66: 'Del Peak 37(18q21.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 37(18Q21.2) MUTATED 30 35 22 4 34 24 4 8
DEL PEAK 37(18Q21.2) WILD-TYPE 13 12 17 41 24 27 0 11

Figure S98.  Get High-res Image Gene #66: 'Del Peak 37(18q21.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 38(18q23) mutation analysis' versus 'CN_CNMF'

P value = 2.42e-16 (Chi-square test), Q value = 1.4e-13

Table S99.  Gene #67: 'Del Peak 38(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 38(18Q23) MUTATED 45 37 28 14 15 5 38
DEL PEAK 38(18Q23) WILD-TYPE 21 4 18 71 7 5 14

Figure S99.  Get High-res Image Gene #67: 'Del Peak 38(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 38(18q23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.38e-11 (Chi-square test), Q value = 7.7e-09

Table S100.  Gene #67: 'Del Peak 38(18q23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 38(18Q23) MUTATED 31 40 23 5 39 23 3 8
DEL PEAK 38(18Q23) WILD-TYPE 12 7 16 40 19 28 1 11

Figure S100.  Get High-res Image Gene #67: 'Del Peak 38(18q23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 40(19q13.43) mutation analysis' versus 'CN_CNMF'

P value = 9.26e-05 (Chi-square test), Q value = 0.045

Table S101.  Gene #69: 'Del Peak 40(19q13.43) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 40(19Q13.43) MUTATED 16 14 16 4 1 2 11
DEL PEAK 40(19Q13.43) WILD-TYPE 50 27 30 81 21 8 41

Figure S101.  Get High-res Image Gene #69: 'Del Peak 40(19q13.43) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 40(19q13.43) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.93e-05 (Chi-square test), Q value = 0.034

Table S102.  Gene #69: 'Del Peak 40(19q13.43) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 40(19Q13.43) MUTATED 7 14 9 3 22 3 0 1
DEL PEAK 40(19Q13.43) WILD-TYPE 36 33 30 42 36 48 4 18

Figure S102.  Get High-res Image Gene #69: 'Del Peak 40(19q13.43) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 41(Xp21.3) mutation analysis' versus 'CN_CNMF'

P value = 7.73e-06 (Chi-square test), Q value = 0.0039

Table S103.  Gene #70: 'Del Peak 41(Xp21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 41(XP21.3) MUTATED 29 22 21 12 9 3 10
DEL PEAK 41(XP21.3) WILD-TYPE 37 19 25 73 13 7 42

Figure S103.  Get High-res Image Gene #70: 'Del Peak 41(Xp21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 42(Xp11.3) mutation analysis' versus 'CN_CNMF'

P value = 9.69e-08 (Chi-square test), Q value = 5.1e-05

Table S104.  Gene #71: 'Del Peak 42(Xp11.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 42(XP11.3) MUTATED 30 22 24 11 9 4 8
DEL PEAK 42(XP11.3) WILD-TYPE 36 19 22 74 13 6 44

Figure S104.  Get High-res Image Gene #71: 'Del Peak 42(Xp11.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 42(Xp11.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.8e-05 (Chi-square test), Q value = 0.029

Table S105.  Gene #71: 'Del Peak 42(Xp11.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 43 47 39 45 58 51 4 19
DEL PEAK 42(XP11.3) MUTATED 15 18 13 7 34 8 2 6
DEL PEAK 42(XP11.3) WILD-TYPE 28 29 26 38 24 43 2 13

Figure S105.  Get High-res Image Gene #71: 'Del Peak 42(Xp11.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 43(Xq21.33) mutation analysis' versus 'CN_CNMF'

P value = 1.07e-06 (Chi-square test), Q value = 0.00055

Table S106.  Gene #72: 'Del Peak 43(Xq21.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 66 41 46 85 22 10 52
DEL PEAK 43(XQ21.33) MUTATED 16 5 20 4 4 0 6
DEL PEAK 43(XQ21.33) WILD-TYPE 50 36 26 81 18 10 46

Figure S106.  Get High-res Image Gene #72: 'Del Peak 43(Xq21.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 43(Xq21.33) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000324 (Fisher's exact test), Q value = 0.15

Table S107.  Gene #72: 'Del Peak 43(Xq21.33) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 127 93
DEL PEAK 43(XQ21.33) MUTATED 12 35 8
DEL PEAK 43(XQ21.33) WILD-TYPE 89 92 85

Figure S107.  Get High-res Image Gene #72: 'Del Peak 43(Xq21.33) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

Methods & Data
Input

  • Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

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

  • Number of patients = 322

  • Number of copy number variation regions = 72

  • Number of molecular subtypes = 8

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle