Correlation between copy number variation genes and molecular subtypes
Stomach Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1NP22PD
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/C1NP22PD
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 6 molecular subtypes across 237 patients, 108 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1p36.22) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 3(1q42.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • Amp Peak 4(3q26.31) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 5(5p13.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 6(6p21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 7(6q12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 8(7p11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 9(7q21.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 10(8p23.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 11(8q24.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 13(9q34.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 14(10q26.13) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 15(11p13) cnvs correlated to 'CN_CNMF'.

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

  • Amp Peak 17(12p12.1) cnvs correlated to 'CN_CNMF'.

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

  • Amp Peak 19(13q12.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 20(13q22.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 21(15q26.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 22(17q12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 23(18q11.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 24(19q12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 25(20q13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 26(Xq27.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 1(1p36.11) cnvs correlated to 'CN_CNMF'.

  • Del Peak 2(1p31.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 6(2q37.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 7(3p26.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 8(3p14.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 9(3q26.31) cnvs correlated to 'CN_CNMF'.

  • Del Peak 10(4p16.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • Del Peak 12(4q35.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • Del Peak 14(6p25.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 15(6q26) cnvs correlated to 'CN_CNMF'.

  • Del Peak 16(6q27) cnvs correlated to 'CN_CNMF'.

  • Del Peak 17(7q31.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 18(7q36.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 19(8p23.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • Del Peak 22(9q21.11) cnvs correlated to 'CN_CNMF'.

  • Del Peak 23(10p14) cnvs correlated to 'CN_CNMF'.

  • Del Peak 24(10q22.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 25(10q23.31) cnvs correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 26(11p15.5) cnvs correlated to 'CN_CNMF'.

  • Del Peak 27(11q23.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 28(12p13.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 29(14q21.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 30(14q32.33) cnvs correlated to 'CN_CNMF'.

  • Del Peak 31(15q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 32(15q15.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 33(16p13.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 34(16q23.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 35(17p12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 36(17q24.3) cnvs correlated to 'CN_CNMF'.

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

  • Del Peak 38(18q22.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 39(19p13.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 40(19q13.11) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 41(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 42(21q11.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 43(22q13.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 44(Xp22.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 45(Xp21.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 46(Xq21.33) cnvs correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 72 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 108 significant findings detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		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
Del Peak 13(5q11 2) 70 (30%) 167 4.27e-19
(1.82e-16) 		4.64e-09
(1.83e-06) 		0.0452
(1.00) 		0.15
(1.00) 		2.27e-05
(0.00804) 		4.05e-06
(0.0015)
Del Peak 39(19p13 3) 71 (30%) 166 2.46e-25
(1.06e-22) 		7.57e-09
(2.96e-06) 		0.347
(1.00) 		0.361
(1.00) 		8.93e-05
(0.0306) 		1.55e-09
(6.12e-07)
Amp Peak 3(1q42 3) 73 (31%) 164 6.71e-13
(2.78e-10) 		0.000639
(0.208) 		0.755
(1.00) 		0.361
(1.00) 		9.69e-05
(0.033) 		0.00587
(1.00)
Amp Peak 24(19q12) 61 (26%) 176 6.26e-10
(2.5e-07) 		0.000449
(0.147) 		0.51
(1.00) 		0.0604
(1.00) 		0.0138
(1.00) 		1.13e-05
(0.00409)
Del Peak 10(4p16 3) 76 (32%) 161 4.98e-12
(2.04e-09) 		2.73e-05
(0.00964) 		0.347
(1.00) 		0.361
(1.00) 		0.00105
(0.337) 		1.5e-06
(0.000567)
Del Peak 11(4q22 1) 91 (38%) 146 2.01e-20
(8.61e-18) 		1.38e-05
(0.00497) 		0.223
(1.00) 		0.543
(1.00) 		0.00334
(1.00) 		0.000205
(0.0682)
Del Peak 12(4q35 1) 87 (37%) 150 8.78e-18
(3.74e-15) 		6.78e-05
(0.0235) 		0.0666
(1.00) 		0.498
(1.00) 		0.0158
(1.00) 		0.000188
(0.063)
Del Peak 19(8p23 2) 56 (24%) 181 8.79e-14
(3.65e-11) 		6.65e-05
(0.0231) 		0.51
(1.00) 		0.899
(1.00) 		0.0474
(1.00) 		0.000177
(0.0595)
Del Peak 25(10q23 31) 54 (23%) 183 2.17e-14
(9.01e-12) 		0.00133
(0.42) 		0.00684
(1.00) 		0.0899
(1.00) 		8.96e-05
(0.0307) 		4.69e-05
(0.0165)
Del Peak 31(15q11 2) 56 (24%) 181 1.01e-11
(4.14e-09) 		0.000138
(0.0465) 		0.00934
(1.00) 		0.011
(1.00) 		0.01
(1.00) 		0.000107
(0.0362)
Del Peak 32(15q15 1) 57 (24%) 180 2.63e-10
(1.06e-07) 		0.000661
(0.215) 		0.0452
(1.00) 		0.0899
(1.00) 		0.0354
(1.00) 		5.96e-05
(0.0207)
Del Peak 35(17p12) 79 (33%) 158 6.8e-23
(2.92e-20) 		2.51e-06
(0.000936) 		0.203
(1.00) 		0.509
(1.00) 		0.00142
(0.447) 		2.01e-05
(0.00713)
Del Peak 40(19q13 11) 30 (13%) 207 8.54e-10
(3.39e-07) 		4.99e-05
(0.0175) 		0.0946
(1.00) 		0.23
(1.00) 		0.00354
(1.00) 		5.22e-05
(0.0183)
Del Peak 43(22q13 31) 70 (30%) 167 7.53e-15
(3.15e-12) 		1.14e-08
(4.46e-06) 		1
(1.00) 		1
(1.00) 		0.00304
(0.926) 		0.00021
(0.0696)
Amp Peak 2(1q21 3) 75 (32%) 162 1.25e-14
(5.22e-12) 		7.53e-06
(0.00276) 		0.215
(1.00) 		0.0203
(1.00) 		0.0008
(0.257) 		0.00164
(0.514)
Amp Peak 6(6p21 1) 60 (25%) 177 6.73e-13
(2.78e-10) 		7.52e-05
(0.0259) 		0.332
(1.00) 		0.678
(1.00) 		0.042
(1.00) 		0.0069
(1.00)
Amp Peak 8(7p11 2) 96 (41%) 141 3.26e-11
(1.32e-08) 		0.000524
(0.171) 		0.547
(1.00) 		0.651
(1.00) 		0.00437
(1.00) 		0.0208
(1.00)
Amp Peak 11(8q24 21) 139 (59%) 98 6.39e-16
(2.69e-13) 		0.000696
(0.226) 		0.281
(1.00) 		0.464
(1.00) 		0.0838
(1.00) 		0.0202
(1.00)
Amp Peak 21(15q26 1) 52 (22%) 185 1.96e-14
(8.16e-12) 		0.000118
(0.0398) 		1
(1.00) 		0.885
(1.00) 		0.0241
(1.00) 		0.0132
(1.00)
Amp Peak 25(20q13 2) 147 (62%) 90 9.23e-20
(3.95e-17) 		8.73e-06
(0.00318) 		0.755
(1.00) 		0.116
(1.00) 		0.0315
(1.00) 		0.0239
(1.00)
Del Peak 14(6p25 3) 48 (20%) 189 2.05e-07
(7.82e-05) 		0.0524
(1.00) 		0.698
(1.00) 		0.424
(1.00) 		0.28
(1.00) 		0.000293
(0.0967)
Del Peak 21(9p21 3) 88 (37%) 149 3.46e-16
(1.47e-13) 		1.63e-08
(6.33e-06) 		0.215
(1.00) 		0.839
(1.00) 		0.00662
(1.00) 		0.00243
(0.751)
Del Peak 27(11q23 2) 43 (18%) 194 0.000245
(0.081) 		0.000202
(0.0675) 		1
(1.00) 		0.215
(1.00) 		0.0607
(1.00) 		0.221
(1.00)
Del Peak 41(20p12 1) 33 (14%) 204 9.18e-06
(0.00333) 		0.000113
(0.0381) 		1
(1.00) 		0.84
(1.00) 		0.0244
(1.00) 		0.016
(1.00)
Amp Peak 1(1p36 22) 24 (10%) 213 7.55e-06
(0.00276) 		0.069
(1.00) 		0.412
(1.00) 		0.557
(1.00) 		0.0421
(1.00) 		0.181
(1.00)
Amp Peak 4(3q26 31) 67 (28%) 170 1.45e-05
(0.00518) 		0.0307
(1.00) 		0.116
(1.00) 		0.142
(1.00) 		0.159
(1.00) 		0.49
(1.00)
Amp Peak 5(5p13 1) 58 (24%) 179 1.17e-12
(4.84e-10) 		0.02
(1.00) 		1
(1.00) 		0.561
(1.00) 		0.0316
(1.00) 		0.00525
(1.00)
Amp Peak 7(6q12) 42 (18%) 195 7.48e-08
(2.87e-05) 		0.0439
(1.00) 		0.51
(1.00) 		0.899
(1.00) 		0.0669
(1.00) 		0.0179
(1.00)
Amp Peak 9(7q21 2) 97 (41%) 140 3.67e-10
(1.47e-07) 		0.0134
(1.00) 		0.547
(1.00) 		0.433
(1.00) 		0.0229
(1.00) 		0.0729
(1.00)
Amp Peak 10(8p23 1) 79 (33%) 158 2.27e-16
(9.64e-14) 		0.96
(1.00) 		0.364
(1.00) 		0.165
(1.00) 		0.558
(1.00) 		0.623
(1.00)
Amp Peak 13(9q34 3) 48 (20%) 189 4.1e-06
(0.00151) 		0.241
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.394
(1.00) 		0.313
(1.00)
Amp Peak 14(10q26 13) 45 (19%) 192 5.82e-05
(0.0203) 		0.0116
(1.00) 		1
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.27
(1.00)
Amp Peak 15(11p13) 38 (16%) 199 0.000315
(0.104) 		0.062
(1.00) 		0.698
(1.00) 		0.293
(1.00) 		0.293
(1.00) 		0.07
(1.00)
Amp Peak 16(11q13 3) 47 (20%) 190 1.35e-06
(0.000509) 		0.0537
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.0107
(1.00) 		0.05
(1.00)
Amp Peak 17(12p12 1) 54 (23%) 183 4.47e-06
(0.00164) 		0.0238
(1.00) 		0.412
(1.00) 		0.557
(1.00) 		0.16
(1.00) 		0.799
(1.00)
Amp Peak 18(12q15) 49 (21%) 188 6.91e-05
(0.0238) 		0.00219
(0.679) 		0.721
(1.00) 		1
(1.00) 		0.475
(1.00) 		0.804
(1.00)
Amp Peak 19(13q12 3) 81 (34%) 156 5.94e-09
(2.33e-06) 		0.00257
(0.79) 		0.223
(1.00) 		0.115
(1.00) 		0.408
(1.00) 		0.151
(1.00)
Amp Peak 20(13q22 1) 88 (37%) 149 2e-08
(7.76e-06) 		0.00482
(1.00) 		0.131
(1.00) 		0.652
(1.00) 		0.323
(1.00) 		0.000777
(0.251)
Amp Peak 22(17q12) 61 (26%) 176 7.74e-12
(3.17e-09) 		0.0395
(1.00) 		0.736
(1.00) 		0.162
(1.00) 		0.0088
(1.00) 		0.00362
(1.00)
Amp Peak 23(18q11 2) 61 (26%) 176 8.77e-07
(0.000332) 		0.00963
(1.00) 		1
(1.00) 		0.616
(1.00) 		0.338
(1.00) 		0.164
(1.00)
Amp Peak 26(Xq27 3) 43 (18%) 194 1.82e-06
(0.000685) 		0.181
(1.00) 		0.457
(1.00) 		0.674
(1.00) 		0.0396
(1.00) 		0.617
(1.00)
Del Peak 1(1p36 11) 63 (27%) 174 2.71e-12
(1.11e-09) 		0.00528
(1.00) 		0.358
(1.00) 		0.538
(1.00) 		0.0698
(1.00) 		0.0118
(1.00)
Del Peak 2(1p31 1) 37 (16%) 200 7.78e-10
(3.1e-07) 		0.191
(1.00) 		0.698
(1.00) 		0.641
(1.00) 		0.241
(1.00) 		0.0311
(1.00)
Del Peak 6(2q37 2) 33 (14%) 204 1.59e-05
(0.00567) 		0.0491
(1.00) 		0.607
(1.00) 		0.643
(1.00) 		0.114
(1.00) 		0.00889
(1.00)
Del Peak 7(3p26 1) 56 (24%) 181 2.49e-10
(1e-07) 		0.00125
(0.398) 		0.31
(1.00) 		0.21
(1.00) 		0.0386
(1.00) 		0.00272
(0.829)
Del Peak 8(3p14 2) 71 (30%) 166 1.9e-11
(7.75e-09) 		0.00468
(1.00) 		0.488
(1.00) 		0.138
(1.00) 		0.205
(1.00) 		0.0138
(1.00)
Del Peak 9(3q26 31) 20 (8%) 217 1.42e-05
(0.00509) 		0.0135
(1.00) 		0.345
(1.00) 		0.356
(1.00) 		0.0599
(1.00) 		0.00659
(1.00)
Del Peak 15(6q26) 47 (20%) 190 9.44e-06
(0.00342) 		0.0154
(1.00) 		0.457
(1.00) 		0.603
(1.00) 		0.223
(1.00) 		0.161
(1.00)
Del Peak 16(6q27) 47 (20%) 190 2.44e-06
(0.000912) 		0.0124
(1.00) 		0.24
(1.00) 		0.293
(1.00) 		0.532
(1.00) 		0.0393
(1.00)
Del Peak 17(7q31 1) 26 (11%) 211 4.84e-06
(0.00178) 		0.0163
(1.00) 		0.412
(1.00) 		0.557
(1.00) 		0.0305
(1.00) 		0.0839
(1.00)
Del Peak 18(7q36 3) 42 (18%) 195 2.54e-10
(1.02e-07) 		0.0013
(0.411) 		0.698
(1.00) 		0.499
(1.00) 		0.179
(1.00) 		0.0017
(0.529)
Del Peak 20(9p23) 90 (38%) 147 5.78e-16
(2.44e-13) 		0.0027
(0.825) 		0.124
(1.00) 		0.449
(1.00) 		0.0331
(1.00) 		0.0262
(1.00)
Del Peak 22(9q21 11) 52 (22%) 185 2.65e-08
(1.02e-05) 		0.00879
(1.00) 		0.698
(1.00) 		0.641
(1.00) 		0.0817
(1.00) 		0.00248
(0.764)
Del Peak 23(10p14) 34 (14%) 203 3.4e-07
(0.000129) 		0.00199
(0.618) 		0.721
(1.00) 		0.885
(1.00) 		0.0167
(1.00) 		0.0459
(1.00)
Del Peak 24(10q22 3) 34 (14%) 203 2.26e-08
(8.73e-06) 		0.0165
(1.00) 		0.132
(1.00) 		0.15
(1.00) 		0.0194
(1.00) 		0.00156
(0.49)
Del Peak 26(11p15 5) 46 (19%) 191 2.23e-09
(8.79e-07) 		0.004
(1.00) 		1
(1.00) 		1
(1.00) 		0.18
(1.00) 		0.00482
(1.00)
Del Peak 28(12p13 2) 34 (14%) 203 5.3e-09
(2.08e-06) 		0.0137
(1.00) 		1
(1.00) 		1
(1.00) 		0.0337
(1.00) 		0.222
(1.00)
Del Peak 29(14q21 1) 52 (22%) 185 3.95e-06
(0.00146) 		0.118
(1.00) 		0.132
(1.00) 		0.674
(1.00) 		0.0343
(1.00) 		0.0177
(1.00)
Del Peak 30(14q32 33) 59 (25%) 178 1.88e-06
(0.000705) 		0.219
(1.00) 		0.0883
(1.00) 		0.458
(1.00) 		0.251
(1.00) 		0.174
(1.00)
Del Peak 33(16p13 3) 34 (14%) 203 3.76e-06
(0.0014) 		0.252
(1.00) 		0.664
(1.00) 		0.73
(1.00) 		0.00711
(1.00) 		0.127
(1.00)
Del Peak 34(16q23 1) 74 (31%) 163 1.79e-05
(0.00638) 		0.688
(1.00) 		0.543
(1.00) 		0.915
(1.00) 		0.665
(1.00) 		0.182
(1.00)
Del Peak 36(17q24 3) 36 (15%) 201 2.57e-08
(9.93e-06) 		0.227
(1.00) 		0.0883
(1.00) 		0.0551
(1.00) 		0.0145
(1.00) 		0.00115
(0.368)
Del Peak 37(18q21 2) 95 (40%) 142 5.1e-16
(2.16e-13) 		0.0144
(1.00) 		0.763
(1.00) 		0.191
(1.00) 		0.112
(1.00) 		0.0142
(1.00)
Del Peak 38(18q22 3) 92 (39%) 145 8.51e-16
(3.57e-13) 		0.0133
(1.00) 		1
(1.00) 		0.917
(1.00) 		0.087
(1.00) 		0.0363
(1.00)
Del Peak 42(21q11 2) 73 (31%) 164 2.9e-11
(1.18e-08) 		0.00347
(1.00) 		0.332
(1.00) 		0.678
(1.00) 		0.0115
(1.00) 		0.275
(1.00)
Del Peak 44(Xp22 2) 38 (16%) 199 3.96e-08
(1.52e-05) 		0.0148
(1.00) 		0.698
(1.00) 		0.732
(1.00) 		0.131
(1.00) 		0.00839
(1.00)
Del Peak 45(Xp21 1) 33 (14%) 204 1.09e-10
(4.42e-08) 		0.0854
(1.00) 		0.281
(1.00) 		0.283
(1.00) 		0.0208
(1.00) 		0.0762
(1.00)
Del Peak 46(Xq21 33) 30 (13%) 207 3.68e-07
(0.00014) 		0.0663
(1.00) 		0.457
(1.00) 		0.674
(1.00) 		0.0496
(1.00) 		0.0108
(1.00)
Amp Peak 12(9p24 1) 30 (13%) 207 0.793
(1.00) 		0.638
(1.00) 		0.698
(1.00) 		0.159
(1.00) 		0.701
(1.00) 		0.353
(1.00)
Del Peak 3(1q44) 14 (6%) 223 0.248
(1.00) 		0.137
(1.00) 		0.412
(1.00) 		0.84
(1.00) 		0.209
(1.00) 		0.0617
(1.00)
Del Peak 4(2q32 1) 28 (12%) 209 0.00333
(1.00) 		0.473
(1.00) 		0.664
(1.00) 		0.73
(1.00) 		0.279
(1.00) 		0.0614
(1.00)
Del Peak 5(2q33 3) 23 (10%) 214 0.00123
(0.392) 		0.39
(1.00) 		0.488
(1.00) 		0.696
(1.00) 		0.236
(1.00)
'Amp Peak 1(1p36.22) mutation analysis' versus 'CN_CNMF'

P value = 7.55e-06 (Fisher's exact test), Q value = 0.0028

Table S1.  Gene #1: 'Amp Peak 1(1p36.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 1(1P36.22) MUTATED 1 21 2
AMP PEAK 1(1P36.22) WILD-TYPE 29 78 106

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1p36.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 2(1q21.3) mutation analysis' versus 'CN_CNMF'

P value = 1.25e-14 (Fisher's exact test), Q value = 5.2e-12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 2(1Q21.3) MUTATED 11 56 8
AMP PEAK 2(1Q21.3) WILD-TYPE 19 43 100

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

'Amp Peak 2(1q21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.53e-06 (Fisher's exact test), Q value = 0.0028

Table S3.  Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
AMP PEAK 2(1Q21.3) MUTATED 2 13 12 31
AMP PEAK 2(1Q21.3) WILD-TYPE 25 39 43 24

Figure S3.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 3(1q42.3) mutation analysis' versus 'CN_CNMF'

P value = 6.71e-13 (Fisher's exact test), Q value = 2.8e-10

Table S4.  Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 3(1Q42.3) MUTATED 10 54 9
AMP PEAK 3(1Q42.3) WILD-TYPE 20 45 99

Figure S4.  Get High-res Image Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 3(1q42.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000639 (Fisher's exact test), Q value = 0.21

Table S5.  Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
AMP PEAK 3(1Q42.3) MUTATED 2 13 15 27
AMP PEAK 3(1Q42.3) WILD-TYPE 25 39 40 28

Figure S5.  Get High-res Image Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 3(1q42.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.69e-05 (Fisher's exact test), Q value = 0.033

Table S6.  Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 55 92
AMP PEAK 3(1Q42.3) MUTATED 19 10 43
AMP PEAK 3(1Q42.3) WILD-TYPE 70 45 49

Figure S6.  Get High-res Image Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Amp Peak 4(3q26.31) mutation analysis' versus 'CN_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.0052

Table S7.  Gene #4: 'Amp Peak 4(3q26.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 4(3Q26.31) MUTATED 10 42 15
AMP PEAK 4(3Q26.31) WILD-TYPE 20 57 93

Figure S7.  Get High-res Image Gene #4: 'Amp Peak 4(3q26.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 5(5p13.1) mutation analysis' versus 'CN_CNMF'

P value = 1.17e-12 (Fisher's exact test), Q value = 4.8e-10

Table S8.  Gene #5: 'Amp Peak 5(5p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 5(5P13.1) MUTATED 3 48 7
AMP PEAK 5(5P13.1) WILD-TYPE 27 51 101

Figure S8.  Get High-res Image Gene #5: 'Amp Peak 5(5p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 6(6p21.1) mutation analysis' versus 'CN_CNMF'

P value = 6.73e-13 (Fisher's exact test), Q value = 2.8e-10

Table S9.  Gene #6: 'Amp Peak 6(6p21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 6(6P21.1) MUTATED 8 47 5
AMP PEAK 6(6P21.1) WILD-TYPE 22 52 103

Figure S9.  Get High-res Image Gene #6: 'Amp Peak 6(6p21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 6(6p21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.52e-05 (Fisher's exact test), Q value = 0.026

Table S10.  Gene #6: 'Amp Peak 6(6p21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
AMP PEAK 6(6P21.1) MUTATED 2 10 7 25
AMP PEAK 6(6P21.1) WILD-TYPE 25 42 48 30

Figure S10.  Get High-res Image Gene #6: 'Amp Peak 6(6p21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 7(6q12) mutation analysis' versus 'CN_CNMF'

P value = 7.48e-08 (Fisher's exact test), Q value = 2.9e-05

Table S11.  Gene #7: 'Amp Peak 7(6q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 7(6Q12) MUTATED 6 32 4
AMP PEAK 7(6Q12) WILD-TYPE 24 67 104

Figure S11.  Get High-res Image Gene #7: 'Amp Peak 7(6q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 8(7p11.2) mutation analysis' versus 'CN_CNMF'

P value = 3.26e-11 (Fisher's exact test), Q value = 1.3e-08

Table S12.  Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 8(7P11.2) MUTATED 14 63 19
AMP PEAK 8(7P11.2) WILD-TYPE 16 36 89

Figure S12.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 8(7p11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000524 (Fisher's exact test), Q value = 0.17

Table S13.  Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
AMP PEAK 8(7P11.2) MUTATED 7 22 12 32
AMP PEAK 8(7P11.2) WILD-TYPE 20 30 43 23

Figure S13.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 9(7q21.2) mutation analysis' versus 'CN_CNMF'

P value = 3.67e-10 (Fisher's exact test), Q value = 1.5e-07

Table S14.  Gene #9: 'Amp Peak 9(7q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 9(7Q21.2) MUTATED 17 60 20
AMP PEAK 9(7Q21.2) WILD-TYPE 13 39 88

Figure S14.  Get High-res Image Gene #9: 'Amp Peak 9(7q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 10(8p23.1) mutation analysis' versus 'CN_CNMF'

P value = 2.27e-16 (Fisher's exact test), Q value = 9.6e-14

Table S15.  Gene #10: 'Amp Peak 10(8p23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 10(8P23.1) MUTATED 30 25 24
AMP PEAK 10(8P23.1) WILD-TYPE 0 74 84

Figure S15.  Get High-res Image Gene #10: 'Amp Peak 10(8p23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 11(8q24.21) mutation analysis' versus 'CN_CNMF'

P value = 6.39e-16 (Fisher's exact test), Q value = 2.7e-13

Table S16.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 11(8Q24.21) MUTATED 29 76 34
AMP PEAK 11(8Q24.21) WILD-TYPE 1 23 74

Figure S16.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 11(8q24.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000696 (Fisher's exact test), Q value = 0.23

Table S17.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
AMP PEAK 11(8Q24.21) MUTATED 8 26 27 41
AMP PEAK 11(8Q24.21) WILD-TYPE 19 26 28 14

Figure S17.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 13(9q34.3) mutation analysis' versus 'CN_CNMF'

P value = 4.1e-06 (Fisher's exact test), Q value = 0.0015

Table S18.  Gene #13: 'Amp Peak 13(9q34.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 13(9Q34.3) MUTATED 4 35 9
AMP PEAK 13(9Q34.3) WILD-TYPE 26 64 99

Figure S18.  Get High-res Image Gene #13: 'Amp Peak 13(9q34.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 14(10q26.13) mutation analysis' versus 'CN_CNMF'

P value = 5.82e-05 (Fisher's exact test), Q value = 0.02

Table S19.  Gene #14: 'Amp Peak 14(10q26.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 14(10Q26.13) MUTATED 3 32 10
AMP PEAK 14(10Q26.13) WILD-TYPE 27 67 98

Figure S19.  Get High-res Image Gene #14: 'Amp Peak 14(10q26.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 15(11p13) mutation analysis' versus 'CN_CNMF'

P value = 0.000315 (Fisher's exact test), Q value = 0.1

Table S20.  Gene #15: 'Amp Peak 15(11p13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 15(11P13) MUTATED 5 26 7
AMP PEAK 15(11P13) WILD-TYPE 25 73 101

Figure S20.  Get High-res Image Gene #15: 'Amp Peak 15(11p13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 1.35e-06 (Fisher's exact test), Q value = 0.00051

Table S21.  Gene #16: 'Amp Peak 16(11q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 16(11Q13.3) MUTATED 6 34 7
AMP PEAK 16(11Q13.3) WILD-TYPE 24 65 101

Figure S21.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 17(12p12.1) mutation analysis' versus 'CN_CNMF'

P value = 4.47e-06 (Fisher's exact test), Q value = 0.0016

Table S22.  Gene #17: 'Amp Peak 17(12p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 17(12P12.1) MUTATED 5 38 11
AMP PEAK 17(12P12.1) WILD-TYPE 25 61 97

Figure S22.  Get High-res Image Gene #17: 'Amp Peak 17(12p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 6.91e-05 (Fisher's exact test), Q value = 0.024

Table S23.  Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 18(12Q15) MUTATED 3 34 12
AMP PEAK 18(12Q15) WILD-TYPE 27 65 96

Figure S23.  Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 19(13q12.3) mutation analysis' versus 'CN_CNMF'

P value = 5.94e-09 (Fisher's exact test), Q value = 2.3e-06

Table S24.  Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 19(13Q12.3) MUTATED 9 55 17
AMP PEAK 19(13Q12.3) WILD-TYPE 21 44 91

Figure S24.  Get High-res Image Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 20(13q22.1) mutation analysis' versus 'CN_CNMF'

P value = 2e-08 (Fisher's exact test), Q value = 7.8e-06

Table S25.  Gene #20: 'Amp Peak 20(13q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 20(13Q22.1) MUTATED 9 58 21
AMP PEAK 20(13Q22.1) WILD-TYPE 21 41 87

Figure S25.  Get High-res Image Gene #20: 'Amp Peak 20(13q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 21(15q26.1) mutation analysis' versus 'CN_CNMF'

P value = 1.96e-14 (Fisher's exact test), Q value = 8.2e-12

Table S26.  Gene #21: 'Amp Peak 21(15q26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 21(15Q26.1) MUTATED 0 46 6
AMP PEAK 21(15Q26.1) WILD-TYPE 30 53 102

Figure S26.  Get High-res Image Gene #21: 'Amp Peak 21(15q26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 21(15q26.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000118 (Fisher's exact test), Q value = 0.04

Table S27.  Gene #21: 'Amp Peak 21(15q26.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
AMP PEAK 21(15Q26.1) MUTATED 0 11 9 22
AMP PEAK 21(15Q26.1) WILD-TYPE 27 41 46 33

Figure S27.  Get High-res Image Gene #21: 'Amp Peak 21(15q26.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 22(17q12) mutation analysis' versus 'CN_CNMF'

P value = 7.74e-12 (Fisher's exact test), Q value = 3.2e-09

Table S28.  Gene #22: 'Amp Peak 22(17q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 22(17Q12) MUTATED 2 49 10
AMP PEAK 22(17Q12) WILD-TYPE 28 50 98

Figure S28.  Get High-res Image Gene #22: 'Amp Peak 22(17q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 23(18q11.2) mutation analysis' versus 'CN_CNMF'

P value = 8.77e-07 (Fisher's exact test), Q value = 0.00033

Table S29.  Gene #23: 'Amp Peak 23(18q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 23(18Q11.2) MUTATED 4 43 14
AMP PEAK 23(18Q11.2) WILD-TYPE 26 56 94

Figure S29.  Get High-res Image Gene #23: 'Amp Peak 23(18q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 24(19q12) mutation analysis' versus 'CN_CNMF'

P value = 6.26e-10 (Fisher's exact test), Q value = 2.5e-07

Table S30.  Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 24(19Q12) MUTATED 3 47 11
AMP PEAK 24(19Q12) WILD-TYPE 27 52 97

Figure S30.  Get High-res Image Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 24(19q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000449 (Fisher's exact test), Q value = 0.15

Table S31.  Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
AMP PEAK 24(19Q12) MUTATED 5 7 11 26
AMP PEAK 24(19Q12) WILD-TYPE 22 45 44 29

Figure S31.  Get High-res Image Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 24(19q12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0041

Table S32.  Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
AMP PEAK 24(19Q12) MUTATED 29 21 10
AMP PEAK 24(19Q12) WILD-TYPE 30 83 63

Figure S32.  Get High-res Image Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 25(20q13.2) mutation analysis' versus 'CN_CNMF'

P value = 9.23e-20 (Fisher's exact test), Q value = 4e-17

Table S33.  Gene #25: 'Amp Peak 25(20q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 25(20Q13.2) MUTATED 19 92 36
AMP PEAK 25(20Q13.2) WILD-TYPE 11 7 72

Figure S33.  Get High-res Image Gene #25: 'Amp Peak 25(20q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 25(20q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.73e-06 (Fisher's exact test), Q value = 0.0032

Table S34.  Gene #25: 'Amp Peak 25(20q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
AMP PEAK 25(20Q13.2) MUTATED 17 25 26 48
AMP PEAK 25(20Q13.2) WILD-TYPE 10 27 29 7

Figure S34.  Get High-res Image Gene #25: 'Amp Peak 25(20q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 26(Xq27.3) mutation analysis' versus 'CN_CNMF'

P value = 1.82e-06 (Fisher's exact test), Q value = 0.00069

Table S35.  Gene #26: 'Amp Peak 26(Xq27.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
AMP PEAK 26(XQ27.3) MUTATED 5 32 6
AMP PEAK 26(XQ27.3) WILD-TYPE 25 67 102

Figure S35.  Get High-res Image Gene #26: 'Amp Peak 26(Xq27.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p36.11) mutation analysis' versus 'CN_CNMF'

P value = 2.71e-12 (Fisher's exact test), Q value = 1.1e-09

Table S36.  Gene #27: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 1(1P36.11) MUTATED 5 50 8
DEL PEAK 1(1P36.11) WILD-TYPE 25 49 100

Figure S36.  Get High-res Image Gene #27: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 2(1p31.1) mutation analysis' versus 'CN_CNMF'

P value = 7.78e-10 (Fisher's exact test), Q value = 3.1e-07

Table S37.  Gene #28: 'Del Peak 2(1p31.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 2(1P31.1) MUTATED 1 33 3
DEL PEAK 2(1P31.1) WILD-TYPE 29 66 105

Figure S37.  Get High-res Image Gene #28: 'Del Peak 2(1p31.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 6(2q37.2) mutation analysis' versus 'CN_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.0057

Table S38.  Gene #32: 'Del Peak 6(2q37.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 6(2Q37.2) MUTATED 4 25 4
DEL PEAK 6(2Q37.2) WILD-TYPE 26 74 104

Figure S38.  Get High-res Image Gene #32: 'Del Peak 6(2q37.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 7(3p26.1) mutation analysis' versus 'CN_CNMF'

P value = 2.49e-10 (Fisher's exact test), Q value = 1e-07

Table S39.  Gene #33: 'Del Peak 7(3p26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 7(3P26.1) MUTATED 5 44 7
DEL PEAK 7(3P26.1) WILD-TYPE 25 55 101

Figure S39.  Get High-res Image Gene #33: 'Del Peak 7(3p26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 8(3p14.2) mutation analysis' versus 'CN_CNMF'

P value = 1.9e-11 (Fisher's exact test), Q value = 7.7e-09

Table S40.  Gene #34: 'Del Peak 8(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 8(3P14.2) MUTATED 9 52 10
DEL PEAK 8(3P14.2) WILD-TYPE 21 47 98

Figure S40.  Get High-res Image Gene #34: 'Del Peak 8(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(3q26.31) mutation analysis' versus 'CN_CNMF'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.0051

Table S41.  Gene #35: 'Del Peak 9(3q26.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 9(3Q26.31) MUTATED 1 18 1
DEL PEAK 9(3Q26.31) WILD-TYPE 29 81 107

Figure S41.  Get High-res Image Gene #35: 'Del Peak 9(3q26.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(4p16.3) mutation analysis' versus 'CN_CNMF'

P value = 4.98e-12 (Fisher's exact test), Q value = 2e-09

Table S42.  Gene #36: 'Del Peak 10(4p16.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 10(4P16.3) MUTATED 5 57 14
DEL PEAK 10(4P16.3) WILD-TYPE 25 42 94

Figure S42.  Get High-res Image Gene #36: 'Del Peak 10(4p16.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(4p16.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.73e-05 (Fisher's exact test), Q value = 0.0096

Table S43.  Gene #36: 'Del Peak 10(4p16.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 10(4P16.3) MUTATED 3 9 15 30
DEL PEAK 10(4P16.3) WILD-TYPE 24 43 40 25

Figure S43.  Get High-res Image Gene #36: 'Del Peak 10(4p16.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 10(4p16.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.5e-06 (Fisher's exact test), Q value = 0.00057

Table S44.  Gene #36: 'Del Peak 10(4p16.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 10(4P16.3) MUTATED 35 21 19
DEL PEAK 10(4P16.3) WILD-TYPE 24 83 54

Figure S44.  Get High-res Image Gene #36: 'Del Peak 10(4p16.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.01e-20 (Fisher's exact test), Q value = 8.6e-18

Table S45.  Gene #37: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 11(4Q22.1) MUTATED 6 72 13
DEL PEAK 11(4Q22.1) WILD-TYPE 24 27 95

Figure S45.  Get High-res Image Gene #37: '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 = 1.38e-05 (Fisher's exact test), Q value = 0.005

Table S46.  Gene #37: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 11(4Q22.1) MUTATED 4 14 17 35
DEL PEAK 11(4Q22.1) WILD-TYPE 23 38 38 20

Figure S46.  Get High-res Image Gene #37: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 0.000205 (Fisher's exact test), Q value = 0.068

Table S47.  Gene #37: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 11(4Q22.1) MUTATED 36 31 23
DEL PEAK 11(4Q22.1) WILD-TYPE 23 73 50

Figure S47.  Get High-res Image Gene #37: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(4q35.1) mutation analysis' versus 'CN_CNMF'

P value = 8.78e-18 (Fisher's exact test), Q value = 3.7e-15

Table S48.  Gene #38: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 12(4Q35.1) MUTATED 5 68 14
DEL PEAK 12(4Q35.1) WILD-TYPE 25 31 94

Figure S48.  Get High-res Image Gene #38: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(4q35.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.78e-05 (Fisher's exact test), Q value = 0.023

Table S49.  Gene #38: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 12(4Q35.1) MUTATED 2 15 19 31
DEL PEAK 12(4Q35.1) WILD-TYPE 25 37 36 24

Figure S49.  Get High-res Image Gene #38: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 12(4q35.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000188 (Fisher's exact test), Q value = 0.063

Table S50.  Gene #38: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 12(4Q35.1) MUTATED 35 30 21
DEL PEAK 12(4Q35.1) WILD-TYPE 24 74 52

Figure S50.  Get High-res Image Gene #38: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.27e-19 (Fisher's exact test), Q value = 1.8e-16

Table S51.  Gene #39: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 13(5Q11.2) MUTATED 4 60 6
DEL PEAK 13(5Q11.2) WILD-TYPE 26 39 102

Figure S51.  Get High-res Image Gene #39: '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 = 4.64e-09 (Fisher's exact test), Q value = 1.8e-06

Table S52.  Gene #39: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 13(5Q11.2) MUTATED 1 12 9 34
DEL PEAK 13(5Q11.2) WILD-TYPE 26 40 46 21

Figure S52.  Get High-res Image Gene #39: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 2.27e-05 (Fisher's exact test), Q value = 0.008

Table S53.  Gene #39: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 55 92
DEL PEAK 13(5Q11.2) MUTATED 24 5 40
DEL PEAK 13(5Q11.2) WILD-TYPE 65 50 52

Figure S53.  Get High-res Image Gene #39: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

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

P value = 4.05e-06 (Fisher's exact test), Q value = 0.0015

Table S54.  Gene #39: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 13(5Q11.2) MUTATED 32 26 11
DEL PEAK 13(5Q11.2) WILD-TYPE 27 78 62

Figure S54.  Get High-res Image Gene #39: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(6p25.3) mutation analysis' versus 'CN_CNMF'

P value = 2.05e-07 (Fisher's exact test), Q value = 7.8e-05

Table S55.  Gene #40: 'Del Peak 14(6p25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 14(6P25.3) MUTATED 2 37 9
DEL PEAK 14(6P25.3) WILD-TYPE 28 62 99

Figure S55.  Get High-res Image Gene #40: 'Del Peak 14(6p25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(6p25.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000293 (Fisher's exact test), Q value = 0.097

Table S56.  Gene #40: 'Del Peak 14(6p25.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 14(6P25.3) MUTATED 23 17 8
DEL PEAK 14(6P25.3) WILD-TYPE 36 87 65

Figure S56.  Get High-res Image Gene #40: 'Del Peak 14(6p25.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(6q26) mutation analysis' versus 'CN_CNMF'

P value = 9.44e-06 (Fisher's exact test), Q value = 0.0034

Table S57.  Gene #41: 'Del Peak 15(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 15(6Q26) MUTATED 4 34 9
DEL PEAK 15(6Q26) WILD-TYPE 26 65 99

Figure S57.  Get High-res Image Gene #41: 'Del Peak 15(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 16(6q27) mutation analysis' versus 'CN_CNMF'

P value = 2.44e-06 (Fisher's exact test), Q value = 0.00091

Table S58.  Gene #42: 'Del Peak 16(6q27) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 16(6Q27) MUTATED 3 35 9
DEL PEAK 16(6Q27) WILD-TYPE 27 64 99

Figure S58.  Get High-res Image Gene #42: 'Del Peak 16(6q27) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 17(7q31.1) mutation analysis' versus 'CN_CNMF'

P value = 4.84e-06 (Fisher's exact test), Q value = 0.0018

Table S59.  Gene #43: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 17(7Q31.1) MUTATED 2 22 2
DEL PEAK 17(7Q31.1) WILD-TYPE 28 77 106

Figure S59.  Get High-res Image Gene #43: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 18(7q36.3) mutation analysis' versus 'CN_CNMF'

P value = 2.54e-10 (Fisher's exact test), Q value = 1e-07

Table S60.  Gene #44: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 18(7Q36.3) MUTATED 3 36 3
DEL PEAK 18(7Q36.3) WILD-TYPE 27 63 105

Figure S60.  Get High-res Image Gene #44: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 19(8p23.2) mutation analysis' versus 'CN_CNMF'

P value = 8.79e-14 (Fisher's exact test), Q value = 3.6e-11

Table S61.  Gene #45: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 19(8P23.2) MUTATED 1 48 7
DEL PEAK 19(8P23.2) WILD-TYPE 29 51 101

Figure S61.  Get High-res Image Gene #45: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 19(8p23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.65e-05 (Fisher's exact test), Q value = 0.023

Table S62.  Gene #45: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 19(8P23.2) MUTATED 0 9 12 23
DEL PEAK 19(8P23.2) WILD-TYPE 27 43 43 32

Figure S62.  Get High-res Image Gene #45: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 19(8p23.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.06

Table S63.  Gene #45: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 19(8P23.2) MUTATED 26 18 11
DEL PEAK 19(8P23.2) WILD-TYPE 33 86 62

Figure S63.  Get High-res Image Gene #45: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.78e-16 (Fisher's exact test), Q value = 2.4e-13

Table S64.  Gene #46: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 20(9P23) MUTATED 11 66 13
DEL PEAK 20(9P23) WILD-TYPE 19 33 95

Figure S64.  Get High-res Image Gene #46: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 3.46e-16 (Fisher's exact test), Q value = 1.5e-13

Table S65.  Gene #47: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 21(9P21.3) MUTATED 9 66 13
DEL PEAK 21(9P21.3) WILD-TYPE 21 33 95

Figure S65.  Get High-res Image Gene #47: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 1.63e-08 (Fisher's exact test), Q value = 6.3e-06

Table S66.  Gene #47: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 21(9P21.3) MUTATED 2 14 16 38
DEL PEAK 21(9P21.3) WILD-TYPE 25 38 39 17

Figure S66.  Get High-res Image Gene #47: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 2.65e-08 (Fisher's exact test), Q value = 1e-05

Table S67.  Gene #48: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 22(9Q21.11) MUTATED 6 39 7
DEL PEAK 22(9Q21.11) WILD-TYPE 24 60 101

Figure S67.  Get High-res Image Gene #48: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 23(10p14) mutation analysis' versus 'CN_CNMF'

P value = 3.4e-07 (Fisher's exact test), Q value = 0.00013

Table S68.  Gene #49: 'Del Peak 23(10p14) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 23(10P14) MUTATED 3 28 3
DEL PEAK 23(10P14) WILD-TYPE 27 71 105

Figure S68.  Get High-res Image Gene #49: 'Del Peak 23(10p14) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 24(10q22.3) mutation analysis' versus 'CN_CNMF'

P value = 2.26e-08 (Fisher's exact test), Q value = 8.7e-06

Table S69.  Gene #50: 'Del Peak 24(10q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 24(10Q22.3) MUTATED 3 29 2
DEL PEAK 24(10Q22.3) WILD-TYPE 27 70 106

Figure S69.  Get High-res Image Gene #50: 'Del Peak 24(10q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 25(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 2.17e-14 (Fisher's exact test), Q value = 9e-12

Table S70.  Gene #51: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 25(10Q23.31) MUTATED 5 46 3
DEL PEAK 25(10Q23.31) WILD-TYPE 25 53 105

Figure S70.  Get High-res Image Gene #51: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 25(10q23.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.96e-05 (Fisher's exact test), Q value = 0.031

Table S71.  Gene #51: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 55 92
DEL PEAK 25(10Q23.31) MUTATED 24 2 28
DEL PEAK 25(10Q23.31) WILD-TYPE 65 53 64

Figure S71.  Get High-res Image Gene #51: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 25(10q23.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.69e-05 (Fisher's exact test), Q value = 0.017

Table S72.  Gene #51: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 25(10Q23.31) MUTATED 22 27 5
DEL PEAK 25(10Q23.31) WILD-TYPE 37 77 68

Figure S72.  Get High-res Image Gene #51: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 2.23e-09 (Fisher's exact test), Q value = 8.8e-07

Table S73.  Gene #52: 'Del Peak 26(11p15.5) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 26(11P15.5) MUTATED 1 38 7
DEL PEAK 26(11P15.5) WILD-TYPE 29 61 101

Figure S73.  Get High-res Image Gene #52: 'Del Peak 26(11p15.5) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(11q23.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000245 (Fisher's exact test), Q value = 0.081

Table S74.  Gene #53: 'Del Peak 27(11q23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 27(11Q23.2) MUTATED 3 30 10
DEL PEAK 27(11Q23.2) WILD-TYPE 27 69 98

Figure S74.  Get High-res Image Gene #53: 'Del Peak 27(11q23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(11q23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.068

Table S75.  Gene #53: 'Del Peak 27(11q23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 27(11Q23.2) MUTATED 1 3 10 19
DEL PEAK 27(11Q23.2) WILD-TYPE 26 49 45 36

Figure S75.  Get High-res Image Gene #53: 'Del Peak 27(11q23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 28(12p13.2) mutation analysis' versus 'CN_CNMF'

P value = 5.3e-09 (Fisher's exact test), Q value = 2.1e-06

Table S76.  Gene #54: 'Del Peak 28(12p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 28(12P13.2) MUTATED 2 30 2
DEL PEAK 28(12P13.2) WILD-TYPE 28 69 106

Figure S76.  Get High-res Image Gene #54: 'Del Peak 28(12p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 29(14q21.1) mutation analysis' versus 'CN_CNMF'

P value = 3.95e-06 (Fisher's exact test), Q value = 0.0015

Table S77.  Gene #55: 'Del Peak 29(14q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 29(14Q21.1) MUTATED 5 37 10
DEL PEAK 29(14Q21.1) WILD-TYPE 25 62 98

Figure S77.  Get High-res Image Gene #55: 'Del Peak 29(14q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 30(14q32.33) mutation analysis' versus 'CN_CNMF'

P value = 1.88e-06 (Fisher's exact test), Q value = 7e-04

Table S78.  Gene #56: 'Del Peak 30(14q32.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 30(14Q32.33) MUTATED 6 41 12
DEL PEAK 30(14Q32.33) WILD-TYPE 24 58 96

Figure S78.  Get High-res Image Gene #56: 'Del Peak 30(14q32.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 31(15q11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.01e-11 (Fisher's exact test), Q value = 4.1e-09

Table S79.  Gene #57: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 31(15Q11.2) MUTATED 3 46 7
DEL PEAK 31(15Q11.2) WILD-TYPE 27 53 101

Figure S79.  Get High-res Image Gene #57: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 31(15q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000138 (Fisher's exact test), Q value = 0.047

Table S80.  Gene #57: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 31(15Q11.2) MUTATED 4 8 8 26
DEL PEAK 31(15Q11.2) WILD-TYPE 23 44 47 29

Figure S80.  Get High-res Image Gene #57: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 31(15q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.036

Table S81.  Gene #57: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 31(15Q11.2) MUTATED 26 21 9
DEL PEAK 31(15Q11.2) WILD-TYPE 33 83 64

Figure S81.  Get High-res Image Gene #57: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(15q15.1) mutation analysis' versus 'CN_CNMF'

P value = 2.63e-10 (Fisher's exact test), Q value = 1.1e-07

Table S82.  Gene #58: 'Del Peak 32(15q15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 32(15Q15.1) MUTATED 4 45 8
DEL PEAK 32(15Q15.1) WILD-TYPE 26 54 100

Figure S82.  Get High-res Image Gene #58: 'Del Peak 32(15q15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 32(15q15.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000661 (Fisher's exact test), Q value = 0.21

Table S83.  Gene #58: 'Del Peak 32(15q15.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 32(15Q15.1) MUTATED 5 8 7 24
DEL PEAK 32(15Q15.1) WILD-TYPE 22 44 48 31

Figure S83.  Get High-res Image Gene #58: 'Del Peak 32(15q15.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 32(15q15.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.96e-05 (Fisher's exact test), Q value = 0.021

Table S84.  Gene #58: 'Del Peak 32(15q15.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 32(15Q15.1) MUTATED 26 23 8
DEL PEAK 32(15Q15.1) WILD-TYPE 33 81 65

Figure S84.  Get High-res Image Gene #58: 'Del Peak 32(15q15.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(16p13.3) mutation analysis' versus 'CN_CNMF'

P value = 3.76e-06 (Fisher's exact test), Q value = 0.0014

Table S85.  Gene #59: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 33(16P13.3) MUTATED 3 27 4
DEL PEAK 33(16P13.3) WILD-TYPE 27 72 104

Figure S85.  Get High-res Image Gene #59: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 34(16q23.1) mutation analysis' versus 'CN_CNMF'

P value = 1.79e-05 (Fisher's exact test), Q value = 0.0064

Table S86.  Gene #60: 'Del Peak 34(16q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 34(16Q23.1) MUTATED 8 47 19
DEL PEAK 34(16Q23.1) WILD-TYPE 22 52 89

Figure S86.  Get High-res Image Gene #60: 'Del Peak 34(16q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 35(17p12) mutation analysis' versus 'CN_CNMF'

P value = 6.8e-23 (Fisher's exact test), Q value = 2.9e-20

Table S87.  Gene #61: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 35(17P12) MUTATED 3 68 8
DEL PEAK 35(17P12) WILD-TYPE 27 31 100

Figure S87.  Get High-res Image Gene #61: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 35(17p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.51e-06 (Fisher's exact test), Q value = 0.00094

Table S88.  Gene #61: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 35(17P12) MUTATED 4 14 11 34
DEL PEAK 35(17P12) WILD-TYPE 23 38 44 21

Figure S88.  Get High-res Image Gene #61: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 35(17p12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.01e-05 (Fisher's exact test), Q value = 0.0071

Table S89.  Gene #61: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 35(17P12) MUTATED 33 32 13
DEL PEAK 35(17P12) WILD-TYPE 26 72 60

Figure S89.  Get High-res Image Gene #61: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 36(17q24.3) mutation analysis' versus 'CN_CNMF'

P value = 2.57e-08 (Fisher's exact test), Q value = 9.9e-06

Table S90.  Gene #62: 'Del Peak 36(17q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 36(17Q24.3) MUTATED 5 29 2
DEL PEAK 36(17Q24.3) WILD-TYPE 25 70 106

Figure S90.  Get High-res Image Gene #62: 'Del Peak 36(17q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 5.1e-16 (Fisher's exact test), Q value = 2.2e-13

Table S91.  Gene #63: 'Del Peak 37(18q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 37(18Q21.2) MUTATED 3 70 22
DEL PEAK 37(18Q21.2) WILD-TYPE 27 29 86

Figure S91.  Get High-res Image Gene #63: 'Del Peak 37(18q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 38(18q22.3) mutation analysis' versus 'CN_CNMF'

P value = 8.51e-16 (Fisher's exact test), Q value = 3.6e-13

Table S92.  Gene #64: 'Del Peak 38(18q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 38(18Q22.3) MUTATED 2 68 22
DEL PEAK 38(18Q22.3) WILD-TYPE 28 31 86

Figure S92.  Get High-res Image Gene #64: 'Del Peak 38(18q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 2.46e-25 (Fisher's exact test), Q value = 1.1e-22

Table S93.  Gene #65: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 39(19P13.3) MUTATED 2 65 4
DEL PEAK 39(19P13.3) WILD-TYPE 28 34 104

Figure S93.  Get High-res Image Gene #65: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 7.57e-09 (Fisher's exact test), Q value = 3e-06

Table S94.  Gene #65: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 39(19P13.3) MUTATED 1 12 8 33
DEL PEAK 39(19P13.3) WILD-TYPE 26 40 47 22

Figure S94.  Get High-res Image Gene #65: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 8.93e-05 (Fisher's exact test), Q value = 0.031

Table S95.  Gene #65: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 55 92
DEL PEAK 39(19P13.3) MUTATED 22 7 41
DEL PEAK 39(19P13.3) WILD-TYPE 67 48 51

Figure S95.  Get High-res Image Gene #65: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

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

P value = 1.55e-09 (Fisher's exact test), Q value = 6.1e-07

Table S96.  Gene #65: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 39(19P13.3) MUTATED 37 23 10
DEL PEAK 39(19P13.3) WILD-TYPE 22 81 63

Figure S96.  Get High-res Image Gene #65: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 40(19q13.11) mutation analysis' versus 'CN_CNMF'

P value = 8.54e-10 (Fisher's exact test), Q value = 3.4e-07

Table S97.  Gene #66: 'Del Peak 40(19q13.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 40(19Q13.11) MUTATED 1 28 1
DEL PEAK 40(19Q13.11) WILD-TYPE 29 71 107

Figure S97.  Get High-res Image Gene #66: 'Del Peak 40(19q13.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 40(19q13.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.99e-05 (Fisher's exact test), Q value = 0.018

Table S98.  Gene #66: 'Del Peak 40(19q13.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 40(19Q13.11) MUTATED 0 6 1 15
DEL PEAK 40(19Q13.11) WILD-TYPE 27 46 54 40

Figure S98.  Get High-res Image Gene #66: 'Del Peak 40(19q13.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 40(19q13.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.22e-05 (Fisher's exact test), Q value = 0.018

Table S99.  Gene #66: 'Del Peak 40(19q13.11) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 40(19Q13.11) MUTATED 18 7 5
DEL PEAK 40(19Q13.11) WILD-TYPE 41 97 68

Figure S99.  Get High-res Image Gene #66: 'Del Peak 40(19q13.11) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 41(20p12.1) mutation analysis' versus 'CN_CNMF'

P value = 9.18e-06 (Fisher's exact test), Q value = 0.0033

Table S100.  Gene #67: 'Del Peak 41(20p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 41(20P12.1) MUTATED 3 26 4
DEL PEAK 41(20P12.1) WILD-TYPE 27 73 104

Figure S100.  Get High-res Image Gene #67: 'Del Peak 41(20p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 41(20p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.038

Table S101.  Gene #67: 'Del Peak 41(20p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 41(20P12.1) MUTATED 2 5 2 18
DEL PEAK 41(20P12.1) WILD-TYPE 25 47 53 37

Figure S101.  Get High-res Image Gene #67: 'Del Peak 41(20p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 42(21q11.2) mutation analysis' versus 'CN_CNMF'

P value = 2.9e-11 (Fisher's exact test), Q value = 1.2e-08

Table S102.  Gene #68: 'Del Peak 42(21q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 42(21Q11.2) MUTATED 7 54 12
DEL PEAK 42(21Q11.2) WILD-TYPE 23 45 96

Figure S102.  Get High-res Image Gene #68: 'Del Peak 42(21q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 43(22q13.31) mutation analysis' versus 'CN_CNMF'

P value = 7.53e-15 (Fisher's exact test), Q value = 3.2e-12

Table S103.  Gene #69: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 43(22Q13.31) MUTATED 6 56 8
DEL PEAK 43(22Q13.31) WILD-TYPE 24 43 100

Figure S103.  Get High-res Image Gene #69: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 43(22q13.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.14e-08 (Fisher's exact test), Q value = 4.5e-06

Table S104.  Gene #69: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 52 55 55
DEL PEAK 43(22Q13.31) MUTATED 0 14 8 31
DEL PEAK 43(22Q13.31) WILD-TYPE 27 38 47 24

Figure S104.  Get High-res Image Gene #69: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 43(22q13.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.07

Table S105.  Gene #69: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 104 73
DEL PEAK 43(22Q13.31) MUTATED 29 28 12
DEL PEAK 43(22Q13.31) WILD-TYPE 30 76 61

Figure S105.  Get High-res Image Gene #69: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 44(Xp22.2) mutation analysis' versus 'CN_CNMF'

P value = 3.96e-08 (Fisher's exact test), Q value = 1.5e-05

Table S106.  Gene #70: 'Del Peak 44(Xp22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 44(XP22.2) MUTATED 1 32 5
DEL PEAK 44(XP22.2) WILD-TYPE 29 67 103

Figure S106.  Get High-res Image Gene #70: 'Del Peak 44(Xp22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 45(Xp21.1) mutation analysis' versus 'CN_CNMF'

P value = 1.09e-10 (Fisher's exact test), Q value = 4.4e-08

Table S107.  Gene #71: 'Del Peak 45(Xp21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 45(XP21.1) MUTATED 0 31 2
DEL PEAK 45(XP21.1) WILD-TYPE 30 68 106

Figure S107.  Get High-res Image Gene #71: 'Del Peak 45(Xp21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 46(Xq21.33) mutation analysis' versus 'CN_CNMF'

P value = 3.68e-07 (Fisher's exact test), Q value = 0.00014

Table S108.  Gene #72: 'Del Peak 46(Xq21.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 99 108
DEL PEAK 46(XQ21.33) MUTATED 0 26 4
DEL PEAK 46(XQ21.33) WILD-TYPE 30 73 104

Figure S108.  Get High-res Image Gene #72: 'Del Peak 46(Xq21.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 237

  • Number of copy number variation regions = 72

  • Number of molecular subtypes = 6

  • 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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