Colon/Rectal Adenocarcinoma: Correlation between copy number variation genes and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

Testing the association between copy number variation of 75 peak regions and 10 molecular subtypes across 575 patients, 166 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1q31.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 2(2q33.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 3(5p12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 5(6p21.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 6(7p21.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 7(8p11.23) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 8(8p11.21) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 9(8q12.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 10(8q24.21) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Amp Peak 12(11p15.5) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 14(13q12.13) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 15(13q12.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 16(13q22.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 18(16p11.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Amp Peak 19(17q12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Amp Peak 20(17q24.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Amp Peak 21(19p13.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 22(19q12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 23(20p11.23) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 24(20p11.21) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 25(20q11.21) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 26(20q12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 27(20q13.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 28(Xq28) cnvs correlated to 'CN_CNMF'.

  • Del Peak 1(1p36.11) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 2(1p33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 3(1p13.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 10(4p16.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • Del Peak 14(5q22.2) cnvs correlated to 'CN_CNMF'.

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

  • Del Peak 19(8p22) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 20(8p11.21) cnvs correlated to 'CN_CNMF'.

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

  • Del Peak 24(10q21.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 25(10q23.31) cnvs correlated to 'CN_CNMF'.

  • Del Peak 26(10q25.2) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 28(12p13.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 29(12q21.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 30(14q22.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • Del Peak 32(15q21.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 33(15q22.33) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 36(17p12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 38(18p11.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 39(18q12.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 40(18q21.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 41(18q22.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 42(19p13.3) cnvs correlated to 'CN_CNMF'.

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

  • Del Peak 44(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 45(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 46(21q11.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 47(22q13.32) 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 75 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 166 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Del Peak 30(14q22 1) 185 (32%) 390 0.000117
(0.0707) 		0.00012
(0.0721) 		1.95e-28
(1.43e-25) 		8.14e-06
(0.0051) 		0.000108
(0.065) 		0.0366
(1.00) 		4.09e-08
(2.71e-05) 		3.08e-05
(0.0189) 		0.127
(1.00) 		0.439
(1.00)
Amp Peak 14(13q12 13) 371 (65%) 204 3.25e-08
(2.16e-05) 		1.57e-06
(0.001) 		6.42e-44
(4.79e-41) 		8.91e-11
(6.11e-08) 		0.078
(1.00) 		0.0601
(1.00) 		8e-11
(5.5e-08) 		4.97e-07
(0.000324) 		0.0136
(1.00) 		0.237
(1.00)
Amp Peak 15(13q12 2) 366 (64%) 209 9.96e-07
(0.000646) 		1.97e-05
(0.0122) 		2.2e-45
(1.65e-42) 		2.31e-11
(1.59e-08) 		0.209
(1.00) 		0.135
(1.00) 		2.13e-10
(1.46e-07) 		1.08e-06
(0.000701) 		0.026
(1.00) 		0.285
(1.00)
Amp Peak 16(13q22 1) 371 (65%) 204 7.58e-06
(0.00477) 		7.24e-05
(0.0439) 		7.69e-42
(5.7e-39) 		2.99e-09
(2.02e-06) 		0.169
(1.00) 		0.0818
(1.00) 		9.82e-10
(6.68e-07) 		5.36e-07
(0.000349) 		0.0301
(1.00) 		0.0471
(1.00)
Amp Peak 24(20p11 21) 339 (59%) 236 0.000239
(0.141) 		1.54e-06
(0.000988) 		8.57e-23
(6.25e-20) 		6.98e-06
(0.00441) 		0.135
(1.00) 		0.268
(1.00) 		4.83e-09
(3.24e-06) 		3.8e-09
(2.55e-06) 		0.107
(1.00) 		0.188
(1.00)
Amp Peak 25(20q11 21) 439 (76%) 136 4.15e-15
(2.93e-12) 		7.48e-14
(5.22e-11) 		1.54e-42
(1.14e-39) 		2.13e-16
(1.52e-13) 		0.121
(1.00) 		0.000913
(0.519) 		1.59e-19
(1.16e-16) 		5.25e-18
(3.78e-15) 		0.124
(1.00) 		0.0189
(1.00)
Amp Peak 26(20q12) 441 (77%) 134 3.23e-16
(2.31e-13) 		3.27e-15
(2.32e-12) 		5.84e-43
(4.34e-40) 		3.56e-15
(2.52e-12) 		0.0547
(1.00) 		0.000897
(0.511) 		5.42e-19
(3.92e-16) 		1.81e-17
(1.3e-14) 		0.065
(1.00) 		0.00779
(1.00)
Amp Peak 27(20q13 32) 444 (77%) 131 2.88e-15
(2.04e-12) 		1.25e-13
(8.71e-11) 		5.66e-43
(4.22e-40) 		3.21e-14
(2.25e-11) 		0.0768
(1.00) 		0.00046
(0.269) 		5.42e-19
(3.92e-16) 		1.81e-17
(1.3e-14) 		0.117
(1.00) 		0.033
(1.00)
Del Peak 36(17p12) 343 (60%) 232 6.93e-08
(4.57e-05) 		2.79e-05
(0.0171) 		2.01e-34
(1.48e-31) 		6.04e-09
(4.03e-06) 		0.412
(1.00) 		0.00486
(1.00) 		1.6e-08
(1.06e-05) 		3.32e-06
(0.00211) 		0.052
(1.00) 		0.673
(1.00)
Del Peak 38(18p11 31) 341 (59%) 234 5.53e-13
(3.84e-10) 		2.35e-09
(1.59e-06) 		1.19e-41
(8.82e-39) 		2.31e-15
(1.65e-12) 		0.627
(1.00) 		0.00179
(0.989) 		1.4e-20
(1.02e-17) 		5.08e-15
(3.58e-12) 		0.0183
(1.00) 		0.386
(1.00)
Del Peak 39(18q12 2) 386 (67%) 189 9.64e-10
(6.57e-07) 		7.31e-08
(4.82e-05) 		1.29e-49
(9.68e-47) 		8.06e-18
(5.8e-15) 		0.268
(1.00) 		0.00412
(1.00) 		2.84e-19
(2.05e-16) 		1.22e-10
(8.36e-08) 		0.00579
(1.00) 		0.059
(1.00)
Del Peak 40(18q21 2) 403 (70%) 172 3.98e-10
(2.72e-07) 		8.24e-08
(5.42e-05) 		1.24e-50
(9.28e-48) 		3.43e-15
(2.43e-12) 		0.0896
(1.00) 		0.00115
(0.648) 		2.83e-15
(2.02e-12) 		1.42e-09
(9.65e-07) 		0.000657
(0.378) 		0.126
(1.00)
Del Peak 41(18q22 1) 398 (69%) 177 2.43e-09
(1.64e-06) 		2.07e-06
(0.00132) 		9.55e-53
(7.16e-50) 		1.37e-15
(9.77e-13) 		0.149
(1.00) 		0.00291
(1.00) 		2.83e-15
(2.02e-12) 		5.84e-09
(3.9e-06) 		0.00128
(0.719) 		0.171
(1.00)
Del Peak 1(1p36 11) 222 (39%) 353 7.45e-05
(0.0452) 		0.00211
(1.00) 		2.21e-13
(1.53e-10) 		2.1e-05
(0.013) 		0.0331
(1.00) 		0.0587
(1.00) 		1.05e-05
(0.00655) 		6.54e-05
(0.0397) 		0.158
(1.00) 		0.0183
(1.00)
Amp Peak 6(7p21 3) 337 (59%) 238 0.000636
(0.368) 		0.00688
(1.00) 		7.91e-22
(5.77e-19) 		7.11e-06
(0.00448) 		0.416
(1.00) 		0.00751
(1.00) 		6.87e-10
(4.69e-07) 		3.15e-06
(0.002) 		0.0224
(1.00) 		0.00259
(1.00)
Amp Peak 12(11p15 5) 129 (22%) 446 4.31e-05
(0.0263) 		0.00115
(0.649) 		1.84e-06
(0.00118) 		0.00344
(1.00) 		0.0108
(1.00) 		0.1
(1.00) 		4.75e-05
(0.029) 		7.68e-06
(0.00482) 		0.352
(1.00) 		0.00906
(1.00)
Amp Peak 23(20p11 23) 301 (52%) 274 0.0117
(1.00) 		0.000401
(0.235) 		5.56e-17
(3.98e-14) 		0.0141
(1.00) 		0.0688
(1.00) 		0.376
(1.00) 		1.06e-05
(0.00663) 		2.29e-05
(0.0141) 		0.353
(1.00) 		0.425
(1.00)
Del Peak 11(4q22 1) 198 (34%) 377 0.0193
(1.00) 		0.0507
(1.00) 		1.25e-14
(8.77e-12) 		7.66e-05
(0.0463) 		0.926
(1.00) 		0.365
(1.00) 		7.1e-06
(0.00448) 		0.00018
(0.107) 		0.148
(1.00) 		0.409
(1.00)
Del Peak 19(8p22) 285 (50%) 290 0.00109
(0.617) 		0.0334
(1.00) 		1.58e-37
(1.17e-34) 		1.32e-06
(0.00085) 		0.277
(1.00) 		0.00111
(0.626) 		1.05e-06
(0.000682) 		0.000223
(0.133) 		0.763
(1.00) 		0.642
(1.00)
Amp Peak 2(2q33 1) 123 (21%) 452 0.048
(1.00) 		0.0609
(1.00) 		1.52e-06
(0.000978) 		0.00502
(1.00) 		0.311
(1.00) 		0.36
(1.00) 		0.000173
(0.103) 		0.000166
(0.0992) 		0.181
(1.00) 		0.00129
(0.725)
Amp Peak 20(17q24 1) 128 (22%) 447 0.00963
(1.00) 		0.00808
(1.00) 		1.54e-08
(1.03e-05) 		0.00035
(0.206) 		0.0887
(1.00) 		0.0124
(1.00) 		0.000201
(0.12) 		0.00309
(1.00) 		0.00127
(0.715) 		0.0419
(1.00)
Del Peak 10(4p16 1) 182 (32%) 393 0.0524
(1.00) 		0.424
(1.00) 		1.65e-12
(1.14e-09) 		0.00203
(1.00) 		0.882
(1.00) 		0.401
(1.00) 		1.32e-06
(0.000853) 		0.000143
(0.086) 		0.622
(1.00) 		0.117
(1.00)
Del Peak 12(4q35 1) 211 (37%) 364 0.0161
(1.00) 		0.185
(1.00) 		1.25e-13
(8.69e-11) 		0.000642
(0.371) 		0.86
(1.00) 		0.669
(1.00) 		5.07e-05
(0.0309) 		3.74e-05
(0.0229) 		0.523
(1.00) 		0.743
(1.00)
Del Peak 18(8p23 2) 272 (47%) 303 0.000586
(0.34) 		0.0322
(1.00) 		2.13e-34
(1.57e-31) 		1.96e-06
(0.00125) 		0.307
(1.00) 		0.0145
(1.00) 		1.52e-05
(0.0094) 		0.000561
(0.326) 		0.802
(1.00) 		0.399
(1.00)
Del Peak 26(10q25 2) 140 (24%) 435 0.312
(1.00) 		0.116
(1.00) 		3.06e-12
(2.11e-09) 		0.105
(1.00) 		0.808
(1.00) 		0.189
(1.00) 		0.000239
(0.141) 		0.000324
(0.191) 		0.972
(1.00) 		0.779
(1.00)
Del Peak 31(15q11 2) 233 (41%) 342 0.000687
(0.394) 		0.0178
(1.00) 		1.2e-23
(8.82e-21) 		0.00572
(1.00) 		0.947
(1.00) 		0.116
(1.00) 		1.41e-06
(0.000909) 		1.38e-05
(0.00854) 		0.478
(1.00) 		0.111
(1.00)
Del Peak 32(15q21 1) 227 (39%) 348 0.00243
(1.00) 		0.0767
(1.00) 		2.43e-21
(1.77e-18) 		0.00358
(1.00) 		0.72
(1.00) 		0.122
(1.00) 		2.2e-07
(0.000144) 		2.3e-05
(0.0141) 		0.742
(1.00) 		0.459
(1.00)
Del Peak 33(15q22 33) 217 (38%) 358 0.000645
(0.372) 		0.00746
(1.00) 		4.49e-23
(3.28e-20) 		0.00084
(0.48) 		0.839
(1.00) 		0.18
(1.00) 		5.81e-09
(3.89e-06) 		5.5e-06
(0.00349) 		0.865
(1.00) 		0.117
(1.00)
Amp Peak 10(8q24 21) 345 (60%) 230 0.24
(1.00) 		0.196
(1.00) 		3.18e-35
(2.35e-32) 		0.00429
(1.00) 		0.345
(1.00) 		0.44
(1.00) 		0.000294
(0.174) 		0.0109
(1.00) 		0.251
(1.00) 		0.176
(1.00)
Amp Peak 18(16p11 2) 161 (28%) 414 0.0134
(1.00) 		0.00695
(1.00) 		1.33e-20
(9.68e-18) 		0.00154
(0.859) 		0.0369
(1.00) 		0.0317
(1.00) 		2.17e-05
(0.0134) 		0.00369
(1.00) 		0.811
(1.00) 		0.11
(1.00)
Amp Peak 19(17q12) 144 (25%) 431 0.015
(1.00) 		0.1
(1.00) 		3.46e-09
(2.33e-06) 		0.00726
(1.00) 		0.506
(1.00) 		0.0442
(1.00) 		0.000424
(0.248) 		0.00212
(1.00) 		0.039
(1.00) 		0.232
(1.00)
Del Peak 2(1p33) 156 (27%) 419 0.0103
(1.00) 		0.0718
(1.00) 		8.95e-13
(6.2e-10) 		0.000371
(0.218) 		0.218
(1.00) 		0.0955
(1.00) 		0.0016
(0.89) 		0.00208
(1.00) 		0.532
(1.00) 		0.0159
(1.00)
Del Peak 13(5q11 2) 140 (24%) 435 0.00191
(1.00) 		0.48
(1.00) 		2.13e-12
(1.47e-09) 		0.00282
(1.00) 		0.793
(1.00) 		0.142
(1.00) 		0.000317
(0.187) 		0.00205
(1.00) 		1
(1.00) 		0.758
(1.00)
Del Peak 44(20p12 1) 179 (31%) 396 0.0234
(1.00) 		0.0236
(1.00) 		6.5e-15
(4.58e-12) 		1.01e-05
(0.00632) 		0.253
(1.00) 		0.00331
(1.00) 		0.0232
(1.00) 		0.0151
(1.00) 		0.223
(1.00) 		0.976
(1.00)
Del Peak 45(20p12 1) 179 (31%) 396 0.0234
(1.00) 		0.0236
(1.00) 		6.5e-15
(4.58e-12) 		1.01e-05
(0.00632) 		0.253
(1.00) 		0.00331
(1.00) 		0.0232
(1.00) 		0.0151
(1.00) 		0.223
(1.00) 		0.976
(1.00)
Amp Peak 1(1q31 1) 134 (23%) 441 0.444
(1.00) 		0.813
(1.00) 		0.000205
(0.122) 		0.722
(1.00) 		0.42
(1.00) 		0.874
(1.00) 		0.0893
(1.00) 		0.32
(1.00) 		0.765
(1.00) 		0.944
(1.00)
Amp Peak 3(5p12) 107 (19%) 468 0.0978
(1.00) 		0.974
(1.00) 		6.55e-06
(0.00414) 		0.794
(1.00) 		0.471
(1.00) 		0.4
(1.00) 		0.102
(1.00) 		0.0189
(1.00) 		0.889
(1.00) 		0.347
(1.00)
Amp Peak 5(6p21 1) 146 (25%) 429 0.0263
(1.00) 		0.00308
(1.00) 		3.97e-14
(2.78e-11) 		0.169
(1.00) 		0.189
(1.00) 		0.578
(1.00) 		0.000931
(0.529) 		0.0151
(1.00) 		0.531
(1.00) 		0.00678
(1.00)
Amp Peak 7(8p11 23) 196 (34%) 379 0.573
(1.00) 		0.4
(1.00) 		2.83e-23
(2.07e-20) 		0.304
(1.00) 		0.884
(1.00) 		0.653
(1.00) 		0.235
(1.00) 		0.781
(1.00) 		0.0154
(1.00) 		0.0772
(1.00)
Amp Peak 8(8p11 21) 238 (41%) 337 0.306
(1.00) 		0.256
(1.00) 		3.33e-31
(2.45e-28) 		0.237
(1.00) 		0.49
(1.00) 		0.613
(1.00) 		0.41
(1.00) 		0.735
(1.00) 		0.0815
(1.00) 		0.201
(1.00)
Amp Peak 9(8q12 1) 309 (54%) 266 0.0798
(1.00) 		0.118
(1.00) 		1.91e-36
(1.41e-33) 		0.0153
(1.00) 		0.101
(1.00) 		0.409
(1.00) 		0.000512
(0.298) 		0.00729
(1.00) 		0.102
(1.00) 		0.146
(1.00)
Amp Peak 21(19p13 2) 97 (17%) 478 0.0439
(1.00) 		0.377
(1.00) 		8.87e-08
(5.83e-05) 		0.0317
(1.00) 		0.622
(1.00) 		0.745
(1.00) 		0.329
(1.00) 		0.418
(1.00) 		0.274
(1.00) 		0.131
(1.00)
Amp Peak 22(19q12) 122 (21%) 453 0.0308
(1.00) 		0.0107
(1.00) 		6.23e-08
(4.12e-05) 		0.251
(1.00) 		0.29
(1.00) 		0.462
(1.00) 		0.0747
(1.00) 		0.0789
(1.00) 		0.71
(1.00) 		0.49
(1.00)
Amp Peak 28(Xq28) 121 (21%) 454 0.345
(1.00) 		0.581
(1.00) 		1.72e-06
(0.0011) 		0.1
(1.00) 		0.000683
(0.392) 		0.133
(1.00) 		0.171
(1.00) 		0.024
(1.00) 		0.99
(1.00) 		0.783
(1.00)
Del Peak 3(1p13 2) 157 (27%) 418 0.189
(1.00) 		0.0923
(1.00) 		3.38e-09
(2.28e-06) 		0.0153
(1.00) 		0.908
(1.00) 		0.069
(1.00) 		0.0132
(1.00) 		0.00062
(0.36) 		0.756
(1.00) 		0.351
(1.00)
Del Peak 14(5q22 2) 172 (30%) 403 0.00141
(0.788) 		0.0581
(1.00) 		2.23e-09
(1.51e-06) 		0.114
(1.00) 		0.884
(1.00) 		0.712
(1.00) 		0.00168
(0.934) 		0.169
(1.00) 		0.771
(1.00) 		0.854
(1.00)
Del Peak 20(8p11 21) 124 (22%) 451 0.0111
(1.00) 		0.126
(1.00) 		4.85e-07
(0.000317) 		0.341
(1.00) 		0.352
(1.00) 		0.159
(1.00) 		0.0621
(1.00) 		0.0497
(1.00) 		0.162
(1.00) 		0.4
(1.00)
Del Peak 23(10p15 3) 102 (18%) 473 0.246
(1.00) 		0.417
(1.00) 		1.38e-07
(9.02e-05) 		0.0288
(1.00) 		0.395
(1.00) 		0.0384
(1.00) 		0.0122
(1.00) 		0.0576
(1.00) 		0.71
(1.00) 		0.302
(1.00)
Del Peak 24(10q21 1) 118 (21%) 457 0.2
(1.00) 		0.111
(1.00) 		3.13e-11
(2.16e-08) 		0.15
(1.00) 		0.476
(1.00) 		0.00976
(1.00) 		0.0728
(1.00) 		0.0438
(1.00) 		0.691
(1.00) 		0.577
(1.00)
Del Peak 25(10q23 31) 145 (25%) 430 0.135
(1.00) 		0.496
(1.00) 		9.09e-08
(5.96e-05) 		0.155
(1.00) 		0.357
(1.00) 		0.00352
(1.00) 		0.00262
(1.00) 		0.0685
(1.00) 		0.762
(1.00) 		0.365
(1.00)
Del Peak 28(12p13 1) 77 (13%) 498 0.00697
(1.00) 		0.0173
(1.00) 		3.89e-08
(2.58e-05) 		0.429
(1.00) 		0.643
(1.00) 		0.664
(1.00) 		0.0571
(1.00) 		0.423
(1.00) 		0.446
(1.00) 		0.919
(1.00)
Del Peak 29(12q21 2) 80 (14%) 495 0.172
(1.00) 		0.0294
(1.00) 		5.52e-07
(0.000359) 		0.348
(1.00) 		0.947
(1.00) 		0.36
(1.00) 		0.0351
(1.00) 		0.294
(1.00) 		0.521
(1.00) 		0.979
(1.00)
Del Peak 42(19p13 3) 92 (16%) 483 0.0887
(1.00) 		0.684
(1.00) 		1.35e-05
(0.00841) 		0.825
(1.00) 		0.493
(1.00) 		0.456
(1.00) 		0.0329
(1.00) 		0.00869
(1.00) 		0.579
(1.00) 		0.911
(1.00)
Del Peak 43(19q13 43) 68 (12%) 507 0.951
(1.00) 		0.698
(1.00) 		0.00011
(0.0666) 		0.6
(1.00) 		1
(1.00) 		0.323
(1.00) 		0.00935
(1.00) 		0.00916
(1.00) 		0.255
(1.00) 		0.502
(1.00)
Del Peak 46(21q11 2) 195 (34%) 380 0.00177
(0.984) 		0.126
(1.00) 		4.07e-09
(2.73e-06) 		0.0109
(1.00) 		0.501
(1.00) 		0.0493
(1.00) 		0.000647
(0.373) 		0.00527
(1.00) 		0.234
(1.00) 		0.0494
(1.00)
Del Peak 47(22q13 32) 204 (35%) 371 0.0226
(1.00) 		0.00461
(1.00) 		9.83e-15
(6.9e-12) 		0.0299
(1.00) 		0.118
(1.00) 		0.532
(1.00) 		0.000824
(0.471) 		0.0349
(1.00) 		0.696
(1.00) 		0.0115
(1.00)
Amp Peak 4(5q22 3) 59 (10%) 516 0.894
(1.00) 		1
(1.00) 		0.0037
(1.00) 		0.32
(1.00) 		0.69
(1.00) 		0.769
(1.00) 		0.248
(1.00) 		0.02
(1.00) 		0.46
(1.00) 		0.894
(1.00)
Amp Peak 11(10q22 3) 35 (6%) 540 0.903
(1.00) 		0.145
(1.00) 		0.655
(1.00) 		0.56
(1.00) 		0.38
(1.00) 		0.341
(1.00) 		0.579
(1.00) 		0.187
(1.00) 		0.587
(1.00) 		0.281
(1.00)
Amp Peak 13(12p13 32) 144 (25%) 431 0.181
(1.00) 		0.786
(1.00) 		0.252
(1.00) 		0.137
(1.00) 		1
(1.00) 		0.874
(1.00) 		0.205
(1.00) 		0.348
(1.00) 		0.676
(1.00) 		0.886
(1.00)
Amp Peak 17(15q26 1) 43 (7%) 532 0.526
(1.00) 		0.394
(1.00) 		0.249
(1.00) 		0.842
(1.00) 		0.64
(1.00) 		0.591
(1.00) 		0.191
(1.00) 		0.241
(1.00) 		0.926
(1.00) 		1
(1.00)
Del Peak 4(2p12) 20 (3%) 555 1
(1.00) 		0.435
(1.00) 		0.00194
(1.00) 		0.0111
(1.00) 		0.48
(1.00) 		0.807
(1.00) 		0.173
(1.00) 		0.738
(1.00) 		0.0165
(1.00) 		0.0215
(1.00)
Del Peak 5(2q22 1) 33 (6%) 542 0.927
(1.00) 		0.851
(1.00) 		0.146
(1.00) 		0.833
(1.00) 		0.363
(1.00) 		0.618
(1.00) 		0.974
(1.00) 		0.797
(1.00) 		0.316
(1.00) 		0.272
(1.00)
Del Peak 6(2q37 2) 30 (5%) 545 0.924
(1.00) 		0.691
(1.00) 		0.285
(1.00) 		0.833
(1.00) 		0.205
(1.00) 		0.444
(1.00) 		0.56
(1.00) 		0.0948
(1.00) 		0.244
(1.00) 		0.364
(1.00)
Del Peak 7(3p26 3) 84 (15%) 491 0.105
(1.00) 		0.819
(1.00) 		0.163
(1.00) 		0.357
(1.00) 		0.984
(1.00) 		0.346
(1.00) 		0.28
(1.00) 		0.0366
(1.00) 		0.277
(1.00) 		0.728
(1.00)
Del Peak 8(3p14 2) 104 (18%) 471 0.475
(1.00) 		0.9
(1.00) 		0.932
(1.00) 		0.597
(1.00) 		0.928
(1.00) 		0.784
(1.00) 		0.553
(1.00) 		0.663
(1.00) 		0.0595
(1.00) 		0.918
(1.00)
Del Peak 9(3q26 31) 56 (10%) 519 0.297
(1.00) 		0.554
(1.00) 		0.448
(1.00) 		0.373
(1.00) 		0.134
(1.00) 		0.676
(1.00) 		0.308
(1.00) 		0.0516
(1.00) 		0.0934
(1.00) 		0.123
(1.00)
Del Peak 15(6p25 3) 78 (14%) 497 0.84
(1.00) 		0.599
(1.00) 		0.0849
(1.00) 		0.262
(1.00) 		1
(1.00) 		0.315
(1.00) 		0.961
(1.00) 		0.385
(1.00) 		0.61
(1.00) 		0.957
(1.00)
Del Peak 16(6q26) 90 (16%) 485 0.886
(1.00) 		0.698
(1.00) 		0.0401
(1.00) 		0.762
(1.00) 		0.235
(1.00) 		0.582
(1.00) 		0.919
(1.00) 		0.948
(1.00) 		0.223
(1.00) 		0.507
(1.00)
Del Peak 17(7q31 1) 15 (3%) 560 0.103
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.434
(1.00) 		0.51
(1.00) 		0.66
(1.00) 		0.714
(1.00) 		0.235
(1.00) 		0.498
(1.00)
Del Peak 21(8q11 1) 44 (8%) 531 0.272
(1.00) 		0.687
(1.00) 		0.00266
(1.00) 		0.661
(1.00) 		0.757
(1.00) 		0.0965
(1.00) 		0.315
(1.00) 		0.32
(1.00) 		0.0819
(1.00) 		0.0193
(1.00)
Del Peak 22(9p24 2) 78 (14%) 497 0.256
(1.00) 		0.15
(1.00) 		0.00178
(0.988) 		0.0506
(1.00) 		0.297
(1.00) 		0.541
(1.00) 		0.0295
(1.00) 		0.00241
(1.00) 		0.296
(1.00) 		0.243
(1.00)
Del Peak 27(11q22 3) 104 (18%) 471 0.585
(1.00) 		0.53
(1.00) 		0.0385
(1.00) 		0.125
(1.00) 		0.454
(1.00) 		0.184
(1.00) 		0.0365
(1.00) 		0.524
(1.00) 		0.657
(1.00) 		0.363
(1.00)
Del Peak 34(16p13 3) 58 (10%) 517 0.142
(1.00) 		0.382
(1.00) 		0.215
(1.00) 		0.676
(1.00) 		0.811
(1.00) 		0.784
(1.00) 		0.927
(1.00) 		0.176
(1.00) 		0.637
(1.00) 		0.595
(1.00)
Del Peak 35(16q23 1) 72 (13%) 503 0.0646
(1.00) 		0.00115
(0.648) 		0.179
(1.00) 		0.327
(1.00) 		0.867
(1.00) 		0.261
(1.00) 		0.271
(1.00) 		0.23
(1.00) 		0.805
(1.00) 		0.632
(1.00)
Del Peak 37(17q24 3) 84 (15%) 491 0.905
(1.00) 		0.876
(1.00) 		0.0296
(1.00) 		0.528
(1.00) 		0.498
(1.00) 		0.258
(1.00) 		0.184
(1.00) 		0.0781
(1.00) 		0.919
(1.00) 		0.425
(1.00)
'Amp Peak 1(1q31.1) mutation analysis' versus 'CN_CNMF'

P value = 0.000205 (Fisher's exact test), Q value = 0.12

Table S1.  Gene #1: 'Amp Peak 1(1q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 1(1Q31.1) MUTATED 59 34 26 15
AMP PEAK 1(1Q31.1) WILD-TYPE 141 200 74 26

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 2(2q33.1) mutation analysis' versus 'CN_CNMF'

P value = 1.52e-06 (Fisher's exact test), Q value = 0.00098

Table S2.  Gene #2: 'Amp Peak 2(2q33.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 2(2Q33.1) MUTATED 59 27 21 16
AMP PEAK 2(2Q33.1) WILD-TYPE 141 207 79 25

Figure S2.  Get High-res Image Gene #2: 'Amp Peak 2(2q33.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 2(2q33.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.1

Table S3.  Gene #2: 'Amp Peak 2(2q33.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 2(2Q33.1) MUTATED 6 30 13 5
AMP PEAK 2(2Q33.1) WILD-TYPE 32 51 43 61

Figure S3.  Get High-res Image Gene #2: 'Amp Peak 2(2q33.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 2(2q33.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000166 (Fisher's exact test), Q value = 0.099

Table S4.  Gene #2: 'Amp Peak 2(2q33.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
AMP PEAK 2(2Q33.1) MUTATED 21 5 28
AMP PEAK 2(2Q33.1) WILD-TYPE 74 62 51

Figure S4.  Get High-res Image Gene #2: 'Amp Peak 2(2q33.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(5p12) mutation analysis' versus 'CN_CNMF'

P value = 6.55e-06 (Fisher's exact test), Q value = 0.0041

Table S5.  Gene #3: 'Amp Peak 3(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 3(5P12) MUTATED 51 21 24 11
AMP PEAK 3(5P12) WILD-TYPE 149 213 76 30

Figure S5.  Get High-res Image Gene #3: 'Amp Peak 3(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 5(6p21.1) mutation analysis' versus 'CN_CNMF'

P value = 3.97e-14 (Fisher's exact test), Q value = 2.8e-11

Table S6.  Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 5(6P21.1) MUTATED 83 22 27 14
AMP PEAK 5(6P21.1) WILD-TYPE 117 212 73 27

Figure S6.  Get High-res Image Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 6(7p21.3) mutation analysis' versus 'CN_CNMF'

P value = 7.91e-22 (Fisher's exact test), Q value = 5.8e-19

Table S7.  Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 6(7P21.3) MUTATED 157 81 66 33
AMP PEAK 6(7P21.3) WILD-TYPE 43 153 34 8

Figure S7.  Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 6(7p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.11e-06 (Fisher's exact test), Q value = 0.0045

Table S8.  Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
AMP PEAK 6(7P21.3) MUTATED 112 58 51
AMP PEAK 6(7P21.3) WILD-TYPE 31 55 40

Figure S8.  Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 6(7p21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.87e-10 (Fisher's exact test), Q value = 4.7e-07

Table S9.  Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 6(7P21.3) MUTATED 27 67 38 20
AMP PEAK 6(7P21.3) WILD-TYPE 11 14 18 46

Figure S9.  Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 6(7p21.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.15e-06 (Fisher's exact test), Q value = 0.002

Table S10.  Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
AMP PEAK 6(7P21.3) MUTATED 64 26 62
AMP PEAK 6(7P21.3) WILD-TYPE 31 41 17

Figure S10.  Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(8p11.23) mutation analysis' versus 'CN_CNMF'

P value = 2.83e-23 (Fisher's exact test), Q value = 2.1e-20

Table S11.  Gene #7: 'Amp Peak 7(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 7(8P11.23) MUTATED 56 44 76 20
AMP PEAK 7(8P11.23) WILD-TYPE 144 190 24 21

Figure S11.  Get High-res Image Gene #7: 'Amp Peak 7(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 8(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 3.33e-31 (Fisher's exact test), Q value = 2.5e-28

Table S12.  Gene #8: 'Amp Peak 8(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 8(8P11.21) MUTATED 75 51 89 23
AMP PEAK 8(8P11.21) WILD-TYPE 125 183 11 18

Figure S12.  Get High-res Image Gene #8: 'Amp Peak 8(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 9(8q12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.91e-36 (Fisher's exact test), Q value = 1.4e-33

Table S13.  Gene #9: 'Amp Peak 9(8q12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 9(8Q12.1) MUTATED 109 69 97 34
AMP PEAK 9(8Q12.1) WILD-TYPE 91 165 3 7

Figure S13.  Get High-res Image Gene #9: 'Amp Peak 9(8q12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 10(8q24.21) mutation analysis' versus 'CN_CNMF'

P value = 3.18e-35 (Fisher's exact test), Q value = 2.3e-32

Table S14.  Gene #10: 'Amp Peak 10(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 10(8Q24.21) MUTATED 129 82 99 35
AMP PEAK 10(8Q24.21) WILD-TYPE 71 152 1 6

Figure S14.  Get High-res Image Gene #10: 'Amp Peak 10(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 10(8q24.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.17

Table S15.  Gene #10: 'Amp Peak 10(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 10(8Q24.21) MUTATED 20 65 31 33
AMP PEAK 10(8Q24.21) WILD-TYPE 18 16 25 33

Figure S15.  Get High-res Image Gene #10: 'Amp Peak 10(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 12(11p15.5) mutation analysis' versus 'MRNA_CNMF'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.026

Table S16.  Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
AMP PEAK 12(11P15.5) MUTATED 3 21 24 3
AMP PEAK 12(11P15.5) WILD-TYPE 42 41 45 36

Figure S16.  Get High-res Image Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 12(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 1.84e-06 (Fisher's exact test), Q value = 0.0012

Table S17.  Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 12(11P15.5) MUTATED 58 31 21 19
AMP PEAK 12(11P15.5) WILD-TYPE 142 203 79 22

Figure S17.  Get High-res Image Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 12(11p15.5) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.75e-05 (Fisher's exact test), Q value = 0.029

Table S18.  Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 12(11P15.5) MUTATED 6 28 11 3
AMP PEAK 12(11P15.5) WILD-TYPE 32 53 45 63

Figure S18.  Get High-res Image Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 12(11p15.5) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.68e-06 (Fisher's exact test), Q value = 0.0048

Table S19.  Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
AMP PEAK 12(11P15.5) MUTATED 17 3 28
AMP PEAK 12(11P15.5) WILD-TYPE 78 64 51

Figure S19.  Get High-res Image Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(13q12.13) mutation analysis' versus 'MRNA_CNMF'

P value = 3.25e-08 (Fisher's exact test), Q value = 2.2e-05

Table S20.  Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
AMP PEAK 14(13Q12.13) MUTATED 20 49 57 14
AMP PEAK 14(13Q12.13) WILD-TYPE 25 13 12 25

Figure S20.  Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 14(13q12.13) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.57e-06 (Fisher's exact test), Q value = 0.001

Table S21.  Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
AMP PEAK 14(13Q12.13) MUTATED 24 82 34
AMP PEAK 14(13Q12.13) WILD-TYPE 37 32 6

Figure S21.  Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 14(13q12.13) mutation analysis' versus 'CN_CNMF'

P value = 6.42e-44 (Fisher's exact test), Q value = 4.8e-41

Table S22.  Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 14(13Q12.13) MUTATED 194 86 66 25
AMP PEAK 14(13Q12.13) WILD-TYPE 6 148 34 16

Figure S22.  Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 14(13q12.13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.91e-11 (Fisher's exact test), Q value = 6.1e-08

Table S23.  Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
AMP PEAK 14(13Q12.13) MUTATED 122 55 50
AMP PEAK 14(13Q12.13) WILD-TYPE 21 58 41

Figure S23.  Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 14(13q12.13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8e-11 (Fisher's exact test), Q value = 5.5e-08

Table S24.  Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 14(13Q12.13) MUTATED 29 67 37 19
AMP PEAK 14(13Q12.13) WILD-TYPE 9 14 19 47

Figure S24.  Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 14(13q12.13) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.97e-07 (Fisher's exact test), Q value = 0.00032

Table S25.  Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
AMP PEAK 14(13Q12.13) MUTATED 64 25 63
AMP PEAK 14(13Q12.13) WILD-TYPE 31 42 16

Figure S25.  Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(13q12.2) mutation analysis' versus 'MRNA_CNMF'

P value = 9.96e-07 (Fisher's exact test), Q value = 0.00065

Table S26.  Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
AMP PEAK 15(13Q12.2) MUTATED 20 48 55 15
AMP PEAK 15(13Q12.2) WILD-TYPE 25 14 14 24

Figure S26.  Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 15(13q12.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.012

Table S27.  Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
AMP PEAK 15(13Q12.2) MUTATED 25 80 33
AMP PEAK 15(13Q12.2) WILD-TYPE 36 34 7

Figure S27.  Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 15(13q12.2) mutation analysis' versus 'CN_CNMF'

P value = 2.2e-45 (Fisher's exact test), Q value = 1.6e-42

Table S28.  Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 15(13Q12.2) MUTATED 194 83 64 25
AMP PEAK 15(13Q12.2) WILD-TYPE 6 151 36 16

Figure S28.  Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 15(13q12.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.31e-11 (Fisher's exact test), Q value = 1.6e-08

Table S29.  Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
AMP PEAK 15(13Q12.2) MUTATED 122 53 50
AMP PEAK 15(13Q12.2) WILD-TYPE 21 60 41

Figure S29.  Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 15(13q12.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.13e-10 (Fisher's exact test), Q value = 1.5e-07

Table S30.  Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 15(13Q12.2) MUTATED 29 66 37 19
AMP PEAK 15(13Q12.2) WILD-TYPE 9 15 19 47

Figure S30.  Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 15(13q12.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.08e-06 (Fisher's exact test), Q value = 7e-04

Table S31.  Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
AMP PEAK 15(13Q12.2) MUTATED 64 25 62
AMP PEAK 15(13Q12.2) WILD-TYPE 31 42 17

Figure S31.  Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 16(13q22.1) mutation analysis' versus 'MRNA_CNMF'

P value = 7.58e-06 (Fisher's exact test), Q value = 0.0048

Table S32.  Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
AMP PEAK 16(13Q22.1) MUTATED 21 47 54 15
AMP PEAK 16(13Q22.1) WILD-TYPE 24 15 15 24

Figure S32.  Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 16(13q22.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 7.24e-05 (Fisher's exact test), Q value = 0.044

Table S33.  Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
AMP PEAK 16(13Q22.1) MUTATED 25 81 31
AMP PEAK 16(13Q22.1) WILD-TYPE 36 33 9

Figure S33.  Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 16(13q22.1) mutation analysis' versus 'CN_CNMF'

P value = 7.69e-42 (Fisher's exact test), Q value = 5.7e-39

Table S34.  Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 16(13Q22.1) MUTATED 193 88 66 24
AMP PEAK 16(13Q22.1) WILD-TYPE 7 146 34 17

Figure S34.  Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 16(13q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.99e-09 (Fisher's exact test), Q value = 2e-06

Table S35.  Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
AMP PEAK 16(13Q22.1) MUTATED 121 58 51
AMP PEAK 16(13Q22.1) WILD-TYPE 22 55 40

Figure S35.  Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 16(13q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.82e-10 (Fisher's exact test), Q value = 6.7e-07

Table S36.  Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 16(13Q22.1) MUTATED 30 69 35 23
AMP PEAK 16(13Q22.1) WILD-TYPE 8 12 21 43

Figure S36.  Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 16(13q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.36e-07 (Fisher's exact test), Q value = 0.00035

Table S37.  Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
AMP PEAK 16(13Q22.1) MUTATED 65 27 65
AMP PEAK 16(13Q22.1) WILD-TYPE 30 40 14

Figure S37.  Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 18(16p11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.33e-20 (Fisher's exact test), Q value = 9.7e-18

Table S38.  Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 18(16P11.2) MUTATED 101 22 25 13
AMP PEAK 18(16P11.2) WILD-TYPE 99 212 75 28

Figure S38.  Get High-res Image Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 18(16p11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.013

Table S39.  Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 18(16P11.2) MUTATED 9 34 16 5
AMP PEAK 18(16P11.2) WILD-TYPE 29 47 40 61

Figure S39.  Get High-res Image Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 19(17q12) mutation analysis' versus 'CN_CNMF'

P value = 3.46e-09 (Fisher's exact test), Q value = 2.3e-06

Table S40.  Gene #19: 'Amp Peak 19(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 19(17Q12) MUTATED 69 27 36 12
AMP PEAK 19(17Q12) WILD-TYPE 131 207 64 29

Figure S40.  Get High-res Image Gene #19: 'Amp Peak 19(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 19(17q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000424 (Fisher's exact test), Q value = 0.25

Table S41.  Gene #19: 'Amp Peak 19(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 19(17Q12) MUTATED 8 33 10 8
AMP PEAK 19(17Q12) WILD-TYPE 30 48 46 58

Figure S41.  Get High-res Image Gene #19: 'Amp Peak 19(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 20(17q24.1) mutation analysis' versus 'CN_CNMF'

P value = 1.54e-08 (Fisher's exact test), Q value = 1e-05

Table S42.  Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 20(17Q24.1) MUTATED 67 24 29 8
AMP PEAK 20(17Q24.1) WILD-TYPE 133 210 71 33

Figure S42.  Get High-res Image Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 20(17q24.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.21

Table S43.  Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
AMP PEAK 20(17Q24.1) MUTATED 47 20 11
AMP PEAK 20(17Q24.1) WILD-TYPE 96 93 80

Figure S43.  Get High-res Image Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 20(17q24.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000201 (Fisher's exact test), Q value = 0.12

Table S44.  Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 20(17Q24.1) MUTATED 9 32 7 8
AMP PEAK 20(17Q24.1) WILD-TYPE 29 49 49 58

Figure S44.  Get High-res Image Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 21(19p13.2) mutation analysis' versus 'CN_CNMF'

P value = 8.87e-08 (Fisher's exact test), Q value = 5.8e-05

Table S45.  Gene #21: 'Amp Peak 21(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 21(19P13.2) MUTATED 54 16 17 10
AMP PEAK 21(19P13.2) WILD-TYPE 146 218 83 31

Figure S45.  Get High-res Image Gene #21: 'Amp Peak 21(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 22(19q12) mutation analysis' versus 'CN_CNMF'

P value = 6.23e-08 (Fisher's exact test), Q value = 4.1e-05

Table S46.  Gene #22: 'Amp Peak 22(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 22(19Q12) MUTATED 68 25 19 10
AMP PEAK 22(19Q12) WILD-TYPE 132 209 81 31

Figure S46.  Get High-res Image Gene #22: 'Amp Peak 22(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 23(20p11.23) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000401 (Fisher's exact test), Q value = 0.23

Table S47.  Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
AMP PEAK 23(20P11.23) MUTATED 18 66 25
AMP PEAK 23(20P11.23) WILD-TYPE 43 48 15

Figure S47.  Get High-res Image Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(20p11.23) mutation analysis' versus 'CN_CNMF'

P value = 5.56e-17 (Fisher's exact test), Q value = 4e-14

Table S48.  Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 23(20P11.23) MUTATED 120 85 55 41
AMP PEAK 23(20P11.23) WILD-TYPE 80 149 45 0

Figure S48.  Get High-res Image Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 23(20p11.23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0066

Table S49.  Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 23(20P11.23) MUTATED 21 54 26 17
AMP PEAK 23(20P11.23) WILD-TYPE 17 27 30 49

Figure S49.  Get High-res Image Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 23(20p11.23) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.29e-05 (Fisher's exact test), Q value = 0.014

Table S50.  Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
AMP PEAK 23(20P11.23) MUTATED 49 18 51
AMP PEAK 23(20P11.23) WILD-TYPE 46 49 28

Figure S50.  Get High-res Image Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(20p11.21) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000239 (Fisher's exact test), Q value = 0.14

Table S51.  Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
AMP PEAK 24(20P11.21) MUTATED 17 42 49 16
AMP PEAK 24(20P11.21) WILD-TYPE 28 20 20 23

Figure S51.  Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 24(20p11.21) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.00099

Table S52.  Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
AMP PEAK 24(20P11.21) MUTATED 19 74 31
AMP PEAK 24(20P11.21) WILD-TYPE 42 40 9

Figure S52.  Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(20p11.21) mutation analysis' versus 'CN_CNMF'

P value = 8.57e-23 (Fisher's exact test), Q value = 6.3e-20

Table S53.  Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 24(20P11.21) MUTATED 150 88 60 41
AMP PEAK 24(20P11.21) WILD-TYPE 50 146 40 0

Figure S53.  Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 24(20p11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.0044

Table S54.  Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
AMP PEAK 24(20P11.21) MUTATED 107 55 45
AMP PEAK 24(20P11.21) WILD-TYPE 36 58 46

Figure S54.  Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 24(20p11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.83e-09 (Fisher's exact test), Q value = 3.2e-06

Table S55.  Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 24(20P11.21) MUTATED 22 63 33 17
AMP PEAK 24(20P11.21) WILD-TYPE 16 18 23 49

Figure S55.  Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 24(20p11.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.8e-09 (Fisher's exact test), Q value = 2.6e-06

Table S56.  Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
AMP PEAK 24(20P11.21) MUTATED 56 18 61
AMP PEAK 24(20P11.21) WILD-TYPE 39 49 18

Figure S56.  Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(20q11.21) mutation analysis' versus 'MRNA_CNMF'

P value = 4.15e-15 (Fisher's exact test), Q value = 2.9e-12

Table S57.  Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
AMP PEAK 25(20Q11.21) MUTATED 19 61 63 21
AMP PEAK 25(20Q11.21) WILD-TYPE 26 1 6 18

Figure S57.  Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 25(20q11.21) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 7.48e-14 (Fisher's exact test), Q value = 5.2e-11

Table S58.  Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
AMP PEAK 25(20Q11.21) MUTATED 24 103 37
AMP PEAK 25(20Q11.21) WILD-TYPE 37 11 3

Figure S58.  Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 25(20q11.21) mutation analysis' versus 'CN_CNMF'

P value = 1.54e-42 (Fisher's exact test), Q value = 1.1e-39

Table S59.  Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 25(20Q11.21) MUTATED 199 116 83 41
AMP PEAK 25(20Q11.21) WILD-TYPE 1 118 17 0

Figure S59.  Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 25(20q11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.13e-16 (Fisher's exact test), Q value = 1.5e-13

Table S60.  Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
AMP PEAK 25(20Q11.21) MUTATED 139 65 62
AMP PEAK 25(20Q11.21) WILD-TYPE 4 48 29

Figure S60.  Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 25(20q11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.59e-19 (Fisher's exact test), Q value = 1.2e-16

Table S61.  Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 25(20Q11.21) MUTATED 31 80 45 22
AMP PEAK 25(20Q11.21) WILD-TYPE 7 1 11 44

Figure S61.  Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 25(20q11.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.25e-18 (Fisher's exact test), Q value = 3.8e-15

Table S62.  Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
AMP PEAK 25(20Q11.21) MUTATED 75 25 78
AMP PEAK 25(20Q11.21) WILD-TYPE 20 42 1

Figure S62.  Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(20q12) mutation analysis' versus 'MRNA_CNMF'

P value = 3.23e-16 (Fisher's exact test), Q value = 2.3e-13

Table S63.  Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
AMP PEAK 26(20Q12) MUTATED 18 61 63 20
AMP PEAK 26(20Q12) WILD-TYPE 27 1 6 19

Figure S63.  Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 26(20q12) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.27e-15 (Fisher's exact test), Q value = 2.3e-12

Table S64.  Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
AMP PEAK 26(20Q12) MUTATED 22 103 37
AMP PEAK 26(20Q12) WILD-TYPE 39 11 3

Figure S64.  Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 26(20q12) mutation analysis' versus 'CN_CNMF'

P value = 5.84e-43 (Fisher's exact test), Q value = 4.3e-40

Table S65.  Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 26(20Q12) MUTATED 199 116 85 41
AMP PEAK 26(20Q12) WILD-TYPE 1 118 15 0

Figure S65.  Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 26(20q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.56e-15 (Fisher's exact test), Q value = 2.5e-12

Table S66.  Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
AMP PEAK 26(20Q12) MUTATED 139 68 63
AMP PEAK 26(20Q12) WILD-TYPE 4 45 28

Figure S66.  Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 26(20q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.42e-19 (Fisher's exact test), Q value = 3.9e-16

Table S67.  Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 26(20Q12) MUTATED 31 80 46 23
AMP PEAK 26(20Q12) WILD-TYPE 7 1 10 43

Figure S67.  Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 26(20q12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.81e-17 (Fisher's exact test), Q value = 1.3e-14

Table S68.  Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
AMP PEAK 26(20Q12) MUTATED 76 26 78
AMP PEAK 26(20Q12) WILD-TYPE 19 41 1

Figure S68.  Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(20q13.32) mutation analysis' versus 'MRNA_CNMF'

P value = 2.88e-15 (Fisher's exact test), Q value = 2e-12

Table S69.  Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
AMP PEAK 27(20Q13.32) MUTATED 19 61 64 22
AMP PEAK 27(20Q13.32) WILD-TYPE 26 1 5 17

Figure S69.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 27(20q13.32) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.25e-13 (Fisher's exact test), Q value = 8.7e-11

Table S70.  Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
AMP PEAK 27(20Q13.32) MUTATED 25 104 37
AMP PEAK 27(20Q13.32) WILD-TYPE 36 10 3

Figure S70.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 27(20q13.32) mutation analysis' versus 'CN_CNMF'

P value = 5.66e-43 (Fisher's exact test), Q value = 4.2e-40

Table S71.  Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 27(20Q13.32) MUTATED 199 117 87 41
AMP PEAK 27(20Q13.32) WILD-TYPE 1 117 13 0

Figure S71.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 27(20q13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.21e-14 (Fisher's exact test), Q value = 2.2e-11

Table S72.  Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
AMP PEAK 27(20Q13.32) MUTATED 138 68 63
AMP PEAK 27(20Q13.32) WILD-TYPE 5 45 28

Figure S72.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 27(20q13.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.42e-19 (Fisher's exact test), Q value = 3.9e-16

Table S73.  Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
AMP PEAK 27(20Q13.32) MUTATED 31 80 46 23
AMP PEAK 27(20Q13.32) WILD-TYPE 7 1 10 43

Figure S73.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 27(20q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.81e-17 (Fisher's exact test), Q value = 1.3e-14

Table S74.  Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
AMP PEAK 27(20Q13.32) MUTATED 76 26 78
AMP PEAK 27(20Q13.32) WILD-TYPE 19 41 1

Figure S74.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 28(Xq28) mutation analysis' versus 'CN_CNMF'

P value = 1.72e-06 (Fisher's exact test), Q value = 0.0011

Table S75.  Gene #28: 'Amp Peak 28(Xq28) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
AMP PEAK 28(XQ28) MUTATED 51 25 32 13
AMP PEAK 28(XQ28) WILD-TYPE 149 209 68 28

Figure S75.  Get High-res Image Gene #28: 'Amp Peak 28(Xq28) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 7.45e-05 (Fisher's exact test), Q value = 0.045

Table S76.  Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
DEL PEAK 1(1P36.11) MUTATED 15 36 34 6
DEL PEAK 1(1P36.11) WILD-TYPE 30 26 35 33

Figure S76.  Get High-res Image Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 2.21e-13 (Fisher's exact test), Q value = 1.5e-10

Table S77.  Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 1(1P36.11) MUTATED 110 52 34 26
DEL PEAK 1(1P36.11) WILD-TYPE 90 182 66 15

Figure S77.  Get High-res Image Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.1e-05 (Fisher's exact test), Q value = 0.013

Table S78.  Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 1(1P36.11) MUTATED 72 26 29
DEL PEAK 1(1P36.11) WILD-TYPE 71 87 62

Figure S78.  Get High-res Image Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0066

Table S79.  Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 1(1P36.11) MUTATED 15 40 27 9
DEL PEAK 1(1P36.11) WILD-TYPE 23 41 29 57

Figure S79.  Get High-res Image Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 6.54e-05 (Fisher's exact test), Q value = 0.04

Table S80.  Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 1(1P36.11) MUTATED 43 11 37
DEL PEAK 1(1P36.11) WILD-TYPE 52 56 42

Figure S80.  Get High-res Image Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p33) mutation analysis' versus 'CN_CNMF'

P value = 8.95e-13 (Fisher's exact test), Q value = 6.2e-10

Table S81.  Gene #30: 'Del Peak 2(1p33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 2(1P33) MUTATED 83 37 14 22
DEL PEAK 2(1P33) WILD-TYPE 117 197 86 19

Figure S81.  Get High-res Image Gene #30: 'Del Peak 2(1p33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 2(1p33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000371 (Fisher's exact test), Q value = 0.22

Table S82.  Gene #30: 'Del Peak 2(1p33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 2(1P33) MUTATED 53 17 25
DEL PEAK 2(1P33) WILD-TYPE 90 96 66

Figure S82.  Get High-res Image Gene #30: 'Del Peak 2(1p33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 3(1p13.2) mutation analysis' versus 'CN_CNMF'

P value = 3.38e-09 (Fisher's exact test), Q value = 2.3e-06

Table S83.  Gene #31: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 3(1P13.2) MUTATED 82 39 18 18
DEL PEAK 3(1P13.2) WILD-TYPE 118 195 82 23

Figure S83.  Get High-res Image Gene #31: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 10(4p16.1) mutation analysis' versus 'CN_CNMF'

P value = 1.65e-12 (Fisher's exact test), Q value = 1.1e-09

Table S84.  Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 10(4P16.1) MUTATED 92 40 26 24
DEL PEAK 10(4P16.1) WILD-TYPE 108 194 74 17

Figure S84.  Get High-res Image Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 10(4p16.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00085

Table S85.  Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 10(4P16.1) MUTATED 15 28 27 5
DEL PEAK 10(4P16.1) WILD-TYPE 23 53 29 61

Figure S85.  Get High-res Image Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 10(4p16.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000143 (Fisher's exact test), Q value = 0.086

Table S86.  Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 10(4P16.1) MUTATED 38 8 29
DEL PEAK 10(4P16.1) WILD-TYPE 57 59 50

Figure S86.  Get High-res Image Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.25e-14 (Fisher's exact test), Q value = 8.8e-12

Table S87.  Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 11(4Q22.1) MUTATED 101 43 28 26
DEL PEAK 11(4Q22.1) WILD-TYPE 99 191 72 15

Figure S87.  Get High-res Image Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 7.66e-05 (Fisher's exact test), Q value = 0.046

Table S88.  Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 11(4Q22.1) MUTATED 64 22 34
DEL PEAK 11(4Q22.1) WILD-TYPE 79 91 57

Figure S88.  Get High-res Image Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 7.1e-06 (Fisher's exact test), Q value = 0.0045

Table S89.  Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 11(4Q22.1) MUTATED 16 33 27 7
DEL PEAK 11(4Q22.1) WILD-TYPE 22 48 29 59

Figure S89.  Get High-res Image Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S90.  Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 11(4Q22.1) MUTATED 42 10 31
DEL PEAK 11(4Q22.1) WILD-TYPE 53 57 48

Figure S90.  Get High-res Image Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.25e-13 (Fisher's exact test), Q value = 8.7e-11

Table S91.  Gene #40: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 12(4Q35.1) MUTATED 105 46 35 25
DEL PEAK 12(4Q35.1) WILD-TYPE 95 188 65 16

Figure S91.  Get High-res Image Gene #40: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 5.07e-05 (Fisher's exact test), Q value = 0.031

Table S92.  Gene #40: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 12(4Q35.1) MUTATED 17 37 28 10
DEL PEAK 12(4Q35.1) WILD-TYPE 21 44 28 56

Figure S92.  Get High-res Image Gene #40: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3.74e-05 (Fisher's exact test), Q value = 0.023

Table S93.  Gene #40: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 12(4Q35.1) MUTATED 42 11 39
DEL PEAK 12(4Q35.1) WILD-TYPE 53 56 40

Figure S93.  Get High-res Image Gene #40: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.13e-12 (Fisher's exact test), Q value = 1.5e-09

Table S94.  Gene #41: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 13(5Q11.2) MUTATED 69 23 27 21
DEL PEAK 13(5Q11.2) WILD-TYPE 131 211 73 20

Figure S94.  Get High-res Image Gene #41: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000317 (Fisher's exact test), Q value = 0.19

Table S95.  Gene #41: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 13(5Q11.2) MUTATED 11 26 16 4
DEL PEAK 13(5Q11.2) WILD-TYPE 27 55 40 62

Figure S95.  Get High-res Image Gene #41: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 14(5q22.2) mutation analysis' versus 'CN_CNMF'

P value = 2.23e-09 (Fisher's exact test), Q value = 1.5e-06

Table S96.  Gene #42: 'Del Peak 14(5q22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 14(5Q22.2) MUTATED 80 38 32 22
DEL PEAK 14(5Q22.2) WILD-TYPE 120 196 68 19

Figure S96.  Get High-res Image Gene #42: 'Del Peak 14(5q22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.13e-34 (Fisher's exact test), Q value = 1.6e-31

Table S97.  Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 18(8P23.2) MUTATED 135 42 77 18
DEL PEAK 18(8P23.2) WILD-TYPE 65 192 23 23

Figure S97.  Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.96e-06 (Fisher's exact test), Q value = 0.0012

Table S98.  Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 18(8P23.2) MUTATED 89 35 38
DEL PEAK 18(8P23.2) WILD-TYPE 54 78 53

Figure S98.  Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.52e-05 (Fisher's exact test), Q value = 0.0094

Table S99.  Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 18(8P23.2) MUTATED 20 48 30 14
DEL PEAK 18(8P23.2) WILD-TYPE 18 33 26 52

Figure S99.  Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 19(8p22) mutation analysis' versus 'CN_CNMF'

P value = 1.58e-37 (Fisher's exact test), Q value = 1.2e-34

Table S100.  Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 19(8P22) MUTATED 142 44 80 19
DEL PEAK 19(8P22) WILD-TYPE 58 190 20 22

Figure S100.  Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 19(8p22) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00085

Table S101.  Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 19(8P22) MUTATED 94 39 39
DEL PEAK 19(8P22) WILD-TYPE 49 74 52

Figure S101.  Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 19(8p22) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00068

Table S102.  Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 19(8P22) MUTATED 22 51 32 14
DEL PEAK 19(8P22) WILD-TYPE 16 30 24 52

Figure S102.  Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 19(8p22) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000223 (Fisher's exact test), Q value = 0.13

Table S103.  Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 19(8P22) MUTATED 56 19 44
DEL PEAK 19(8P22) WILD-TYPE 39 48 35

Figure S103.  Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 4.85e-07 (Fisher's exact test), Q value = 0.00032

Table S104.  Gene #48: 'Del Peak 20(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 20(8P11.21) MUTATED 68 28 18 10
DEL PEAK 20(8P11.21) WILD-TYPE 132 206 82 31

Figure S104.  Get High-res Image Gene #48: 'Del Peak 20(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.38e-07 (Fisher's exact test), Q value = 9e-05

Table S105.  Gene #51: 'Del Peak 23(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 23(10P15.3) MUTATED 41 21 21 19
DEL PEAK 23(10P15.3) WILD-TYPE 159 213 79 22

Figure S105.  Get High-res Image Gene #51: 'Del Peak 23(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 24(10q21.1) mutation analysis' versus 'CN_CNMF'

P value = 3.13e-11 (Fisher's exact test), Q value = 2.2e-08

Table S106.  Gene #52: 'Del Peak 24(10q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 24(10Q21.1) MUTATED 49 20 27 22
DEL PEAK 24(10Q21.1) WILD-TYPE 151 214 73 19

Figure S106.  Get High-res Image Gene #52: 'Del Peak 24(10q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 9.09e-08 (Fisher's exact test), Q value = 6e-05

Table S107.  Gene #53: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 25(10Q23.31) MUTATED 55 35 32 23
DEL PEAK 25(10Q23.31) WILD-TYPE 145 199 68 18

Figure S107.  Get High-res Image Gene #53: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 26(10q25.2) mutation analysis' versus 'CN_CNMF'

P value = 3.06e-12 (Fisher's exact test), Q value = 2.1e-09

Table S108.  Gene #54: 'Del Peak 26(10q25.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 26(10Q25.2) MUTATED 56 30 26 28
DEL PEAK 26(10Q25.2) WILD-TYPE 144 204 74 13

Figure S108.  Get High-res Image Gene #54: 'Del Peak 26(10q25.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 26(10q25.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000239 (Fisher's exact test), Q value = 0.14

Table S109.  Gene #54: 'Del Peak 26(10q25.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 26(10Q25.2) MUTATED 11 26 17 4
DEL PEAK 26(10Q25.2) WILD-TYPE 27 55 39 62

Figure S109.  Get High-res Image Gene #54: 'Del Peak 26(10q25.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 26(10q25.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000324 (Fisher's exact test), Q value = 0.19

Table S110.  Gene #54: 'Del Peak 26(10q25.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 26(10Q25.2) MUTATED 28 5 25
DEL PEAK 26(10Q25.2) WILD-TYPE 67 62 54

Figure S110.  Get High-res Image Gene #54: 'Del Peak 26(10q25.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(12p13.1) mutation analysis' versus 'CN_CNMF'

P value = 3.89e-08 (Fisher's exact test), Q value = 2.6e-05

Table S111.  Gene #56: 'Del Peak 28(12p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 28(12P13.1) MUTATED 44 10 13 10
DEL PEAK 28(12P13.1) WILD-TYPE 156 224 87 31

Figure S111.  Get High-res Image Gene #56: 'Del Peak 28(12p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 29(12q21.2) mutation analysis' versus 'CN_CNMF'

P value = 5.52e-07 (Fisher's exact test), Q value = 0.00036

Table S112.  Gene #57: 'Del Peak 29(12q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 29(12Q21.2) MUTATED 45 13 12 10
DEL PEAK 29(12Q21.2) WILD-TYPE 155 221 88 31

Figure S112.  Get High-res Image Gene #57: 'Del Peak 29(12q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 30(14q22.1) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.071

Table S113.  Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
DEL PEAK 30(14Q22.1) MUTATED 10 31 30 5
DEL PEAK 30(14Q22.1) WILD-TYPE 35 31 39 34

Figure S113.  Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 30(14q22.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.072

Table S114.  Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
DEL PEAK 30(14Q22.1) MUTATED 9 47 20
DEL PEAK 30(14Q22.1) WILD-TYPE 52 67 20

Figure S114.  Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 30(14q22.1) mutation analysis' versus 'CN_CNMF'

P value = 1.95e-28 (Fisher's exact test), Q value = 1.4e-25

Table S115.  Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 30(14Q22.1) MUTATED 124 31 17 13
DEL PEAK 30(14Q22.1) WILD-TYPE 76 203 83 28

Figure S115.  Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 30(14q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.14e-06 (Fisher's exact test), Q value = 0.0051

Table S116.  Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 30(14Q22.1) MUTATED 63 19 24
DEL PEAK 30(14Q22.1) WILD-TYPE 80 94 67

Figure S116.  Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 30(14q22.1) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.065

Table S117.  Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 157 133
DEL PEAK 30(14Q22.1) MUTATED 31 71 29
DEL PEAK 30(14Q22.1) WILD-TYPE 69 86 104

Figure S117.  Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 30(14q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.09e-08 (Fisher's exact test), Q value = 2.7e-05

Table S118.  Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 30(14Q22.1) MUTATED 14 40 16 4
DEL PEAK 30(14Q22.1) WILD-TYPE 24 41 40 62

Figure S118.  Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 30(14q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.08e-05 (Fisher's exact test), Q value = 0.019

Table S119.  Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 30(14Q22.1) MUTATED 34 7 33
DEL PEAK 30(14Q22.1) WILD-TYPE 61 60 46

Figure S119.  Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.2e-23 (Fisher's exact test), Q value = 8.8e-21

Table S120.  Gene #59: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 31(15Q11.2) MUTATED 122 41 40 30
DEL PEAK 31(15Q11.2) WILD-TYPE 78 193 60 11

Figure S120.  Get High-res Image Gene #59: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.41e-06 (Fisher's exact test), Q value = 0.00091

Table S121.  Gene #59: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 31(15Q11.2) MUTATED 16 45 24 9
DEL PEAK 31(15Q11.2) WILD-TYPE 22 36 32 57

Figure S121.  Get High-res Image Gene #59: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0085

Table S122.  Gene #59: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 31(15Q11.2) MUTATED 42 11 41
DEL PEAK 31(15Q11.2) WILD-TYPE 53 56 38

Figure S122.  Get High-res Image Gene #59: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(15q21.1) mutation analysis' versus 'CN_CNMF'

P value = 2.43e-21 (Fisher's exact test), Q value = 1.8e-18

Table S123.  Gene #60: 'Del Peak 32(15q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 32(15Q21.1) MUTATED 117 41 40 29
DEL PEAK 32(15Q21.1) WILD-TYPE 83 193 60 12

Figure S123.  Get High-res Image Gene #60: 'Del Peak 32(15q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 32(15q21.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.2e-07 (Fisher's exact test), Q value = 0.00014

Table S124.  Gene #60: 'Del Peak 32(15q21.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 32(15Q21.1) MUTATED 16 44 21 7
DEL PEAK 32(15Q21.1) WILD-TYPE 22 37 35 59

Figure S124.  Get High-res Image Gene #60: 'Del Peak 32(15q21.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 32(15q21.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.3e-05 (Fisher's exact test), Q value = 0.014

Table S125.  Gene #60: 'Del Peak 32(15q21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 32(15Q21.1) MUTATED 39 10 39
DEL PEAK 32(15Q21.1) WILD-TYPE 56 57 40

Figure S125.  Get High-res Image Gene #60: 'Del Peak 32(15q21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(15q22.33) mutation analysis' versus 'CN_CNMF'

P value = 4.49e-23 (Fisher's exact test), Q value = 3.3e-20

Table S126.  Gene #61: 'Del Peak 33(15q22.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 33(15Q22.33) MUTATED 113 35 40 29
DEL PEAK 33(15Q22.33) WILD-TYPE 87 199 60 12

Figure S126.  Get High-res Image Gene #61: 'Del Peak 33(15q22.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 33(15q22.33) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.81e-09 (Fisher's exact test), Q value = 3.9e-06

Table S127.  Gene #61: 'Del Peak 33(15q22.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 33(15Q22.33) MUTATED 15 44 24 5
DEL PEAK 33(15Q22.33) WILD-TYPE 23 37 32 61

Figure S127.  Get High-res Image Gene #61: 'Del Peak 33(15q22.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 33(15q22.33) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.5e-06 (Fisher's exact test), Q value = 0.0035

Table S128.  Gene #61: 'Del Peak 33(15q22.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 33(15Q22.33) MUTATED 40 9 39
DEL PEAK 33(15Q22.33) WILD-TYPE 55 58 40

Figure S128.  Get High-res Image Gene #61: 'Del Peak 33(15q22.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(17p12) mutation analysis' versus 'MRNA_CNMF'

P value = 6.93e-08 (Fisher's exact test), Q value = 4.6e-05

Table S129.  Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
DEL PEAK 36(17P12) MUTATED 18 50 51 13
DEL PEAK 36(17P12) WILD-TYPE 27 12 18 26

Figure S129.  Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 36(17p12) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.017

Table S130.  Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
DEL PEAK 36(17P12) MUTATED 23 78 31
DEL PEAK 36(17P12) WILD-TYPE 38 36 9

Figure S130.  Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(17p12) mutation analysis' versus 'CN_CNMF'

P value = 2.01e-34 (Fisher's exact test), Q value = 1.5e-31

Table S131.  Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 36(17P12) MUTATED 169 69 75 30
DEL PEAK 36(17P12) WILD-TYPE 31 165 25 11

Figure S131.  Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 36(17p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.04e-09 (Fisher's exact test), Q value = 4e-06

Table S132.  Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 36(17P12) MUTATED 112 50 44
DEL PEAK 36(17P12) WILD-TYPE 31 63 47

Figure S132.  Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 36(17p12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.6e-08 (Fisher's exact test), Q value = 1.1e-05

Table S133.  Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 36(17P12) MUTATED 26 60 35 17
DEL PEAK 36(17P12) WILD-TYPE 12 21 21 49

Figure S133.  Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 36(17p12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.32e-06 (Fisher's exact test), Q value = 0.0021

Table S134.  Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 36(17P12) MUTATED 58 22 58
DEL PEAK 36(17P12) WILD-TYPE 37 45 21

Figure S134.  Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(18p11.31) mutation analysis' versus 'MRNA_CNMF'

P value = 5.53e-13 (Fisher's exact test), Q value = 3.8e-10

Table S135.  Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
DEL PEAK 38(18P11.31) MUTATED 12 52 52 11
DEL PEAK 38(18P11.31) WILD-TYPE 33 10 17 28

Figure S135.  Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 38(18p11.31) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.35e-09 (Fisher's exact test), Q value = 1.6e-06

Table S136.  Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
DEL PEAK 38(18P11.31) MUTATED 16 79 32
DEL PEAK 38(18P11.31) WILD-TYPE 45 35 8

Figure S136.  Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(18p11.31) mutation analysis' versus 'CN_CNMF'

P value = 1.19e-41 (Fisher's exact test), Q value = 8.8e-39

Table S137.  Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 38(18P11.31) MUTATED 176 65 64 36
DEL PEAK 38(18P11.31) WILD-TYPE 24 169 36 5

Figure S137.  Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 38(18p11.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.31e-15 (Fisher's exact test), Q value = 1.7e-12

Table S138.  Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 38(18P11.31) MUTATED 120 40 49
DEL PEAK 38(18P11.31) WILD-TYPE 23 73 42

Figure S138.  Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 38(18p11.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.4e-20 (Fisher's exact test), Q value = 1e-17

Table S139.  Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 38(18P11.31) MUTATED 23 71 36 8
DEL PEAK 38(18P11.31) WILD-TYPE 15 10 20 58

Figure S139.  Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 38(18p11.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.08e-15 (Fisher's exact test), Q value = 3.6e-12

Table S140.  Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 38(18P11.31) MUTATED 62 12 64
DEL PEAK 38(18P11.31) WILD-TYPE 33 55 15

Figure S140.  Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(18q12.2) mutation analysis' versus 'MRNA_CNMF'

P value = 9.64e-10 (Fisher's exact test), Q value = 6.6e-07

Table S141.  Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
DEL PEAK 39(18Q12.2) MUTATED 19 54 56 15
DEL PEAK 39(18Q12.2) WILD-TYPE 26 8 13 24

Figure S141.  Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 39(18q12.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 7.31e-08 (Fisher's exact test), Q value = 4.8e-05

Table S142.  Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
DEL PEAK 39(18Q12.2) MUTATED 23 87 34
DEL PEAK 39(18Q12.2) WILD-TYPE 38 27 6

Figure S142.  Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 39(18q12.2) mutation analysis' versus 'CN_CNMF'

P value = 1.29e-49 (Fisher's exact test), Q value = 9.7e-47

Table S143.  Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 39(18Q12.2) MUTATED 187 76 86 37
DEL PEAK 39(18Q12.2) WILD-TYPE 13 158 14 4

Figure S143.  Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 39(18q12.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.06e-18 (Fisher's exact test), Q value = 5.8e-15

Table S144.  Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 39(18Q12.2) MUTATED 132 51 52
DEL PEAK 39(18Q12.2) WILD-TYPE 11 62 39

Figure S144.  Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 39(18q12.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.84e-19 (Fisher's exact test), Q value = 2.1e-16

Table S145.  Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 39(18Q12.2) MUTATED 29 72 41 12
DEL PEAK 39(18Q12.2) WILD-TYPE 9 9 15 54

Figure S145.  Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 39(18q12.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-10 (Fisher's exact test), Q value = 8.4e-08

Table S146.  Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 39(18Q12.2) MUTATED 67 21 66
DEL PEAK 39(18Q12.2) WILD-TYPE 28 46 13

Figure S146.  Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(18q21.2) mutation analysis' versus 'MRNA_CNMF'

P value = 3.98e-10 (Fisher's exact test), Q value = 2.7e-07

Table S147.  Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
DEL PEAK 40(18Q21.2) MUTATED 19 55 57 16
DEL PEAK 40(18Q21.2) WILD-TYPE 26 7 12 23

Figure S147.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 40(18q21.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 8.24e-08 (Fisher's exact test), Q value = 5.4e-05

Table S148.  Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
DEL PEAK 40(18Q21.2) MUTATED 24 89 34
DEL PEAK 40(18Q21.2) WILD-TYPE 37 25 6

Figure S148.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(18q21.2) mutation analysis' versus 'CN_CNMF'

P value = 1.24e-50 (Fisher's exact test), Q value = 9.3e-48

Table S149.  Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 40(18Q21.2) MUTATED 190 84 91 38
DEL PEAK 40(18Q21.2) WILD-TYPE 10 150 9 3

Figure S149.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 40(18q21.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.43e-15 (Fisher's exact test), Q value = 2.4e-12

Table S150.  Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 40(18Q21.2) MUTATED 134 61 54
DEL PEAK 40(18Q21.2) WILD-TYPE 9 52 37

Figure S150.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 40(18q21.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.83e-15 (Fisher's exact test), Q value = 2e-12

Table S151.  Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 40(18Q21.2) MUTATED 29 73 42 18
DEL PEAK 40(18Q21.2) WILD-TYPE 9 8 14 48

Figure S151.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 40(18q21.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.42e-09 (Fisher's exact test), Q value = 9.7e-07

Table S152.  Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 40(18Q21.2) MUTATED 69 25 68
DEL PEAK 40(18Q21.2) WILD-TYPE 26 42 11

Figure S152.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(18q22.1) mutation analysis' versus 'MRNA_CNMF'

P value = 2.43e-09 (Fisher's exact test), Q value = 1.6e-06

Table S153.  Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
DEL PEAK 41(18Q22.1) MUTATED 19 55 56 17
DEL PEAK 41(18Q22.1) WILD-TYPE 26 7 13 22

Figure S153.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 41(18q22.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.0013

Table S154.  Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
DEL PEAK 41(18Q22.1) MUTATED 26 87 34
DEL PEAK 41(18Q22.1) WILD-TYPE 35 27 6

Figure S154.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 41(18q22.1) mutation analysis' versus 'CN_CNMF'

P value = 9.55e-53 (Fisher's exact test), Q value = 7.2e-50

Table S155.  Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 41(18Q22.1) MUTATED 190 80 89 39
DEL PEAK 41(18Q22.1) WILD-TYPE 10 154 11 2

Figure S155.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 41(18q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.37e-15 (Fisher's exact test), Q value = 9.8e-13

Table S156.  Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 41(18Q22.1) MUTATED 133 59 52
DEL PEAK 41(18Q22.1) WILD-TYPE 10 54 39

Figure S156.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 41(18q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.83e-15 (Fisher's exact test), Q value = 2e-12

Table S157.  Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
DEL PEAK 41(18Q22.1) MUTATED 29 73 42 18
DEL PEAK 41(18Q22.1) WILD-TYPE 9 8 14 48

Figure S157.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 41(18q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.84e-09 (Fisher's exact test), Q value = 3.9e-06

Table S158.  Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
DEL PEAK 41(18Q22.1) MUTATED 68 26 68
DEL PEAK 41(18Q22.1) WILD-TYPE 27 41 11

Figure S158.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 1.35e-05 (Fisher's exact test), Q value = 0.0084

Table S159.  Gene #70: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 42(19P13.3) MUTATED 44 17 21 10
DEL PEAK 42(19P13.3) WILD-TYPE 156 217 79 31

Figure S159.  Get High-res Image Gene #70: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.00011 (Fisher's exact test), Q value = 0.067

Table S160.  Gene #71: 'Del Peak 43(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 43(19Q13.43) MUTATED 28 13 16 11
DEL PEAK 43(19Q13.43) WILD-TYPE 172 221 84 30

Figure S160.  Get High-res Image Gene #71: 'Del Peak 43(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 44(20p12.1) mutation analysis' versus 'CN_CNMF'

P value = 6.5e-15 (Fisher's exact test), Q value = 4.6e-12

Table S161.  Gene #72: 'Del Peak 44(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 44(20P12.1) MUTATED 96 46 37 0
DEL PEAK 44(20P12.1) WILD-TYPE 104 188 63 41

Figure S161.  Get High-res Image Gene #72: 'Del Peak 44(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 44(20p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0063

Table S162.  Gene #72: 'Del Peak 44(20p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 44(20P12.1) MUTATED 63 21 20
DEL PEAK 44(20P12.1) WILD-TYPE 80 92 71

Figure S162.  Get High-res Image Gene #72: 'Del Peak 44(20p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 45(20p12.1) mutation analysis' versus 'CN_CNMF'

P value = 6.5e-15 (Fisher's exact test), Q value = 4.6e-12

Table S163.  Gene #73: 'Del Peak 45(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 45(20P12.1) MUTATED 96 46 37 0
DEL PEAK 45(20P12.1) WILD-TYPE 104 188 63 41

Figure S163.  Get High-res Image Gene #73: 'Del Peak 45(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 45(20p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0063

Table S164.  Gene #73: 'Del Peak 45(20p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
DEL PEAK 45(20P12.1) MUTATED 63 21 20
DEL PEAK 45(20P12.1) WILD-TYPE 80 92 71

Figure S164.  Get High-res Image Gene #73: 'Del Peak 45(20p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 46(21q11.2) mutation analysis' versus 'CN_CNMF'

P value = 4.07e-09 (Fisher's exact test), Q value = 2.7e-06

Table S165.  Gene #74: 'Del Peak 46(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 46(21Q11.2) MUTATED 95 50 28 22
DEL PEAK 46(21Q11.2) WILD-TYPE 105 184 72 19

Figure S165.  Get High-res Image Gene #74: 'Del Peak 46(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 47(22q13.32) mutation analysis' versus 'CN_CNMF'

P value = 9.83e-15 (Fisher's exact test), Q value = 6.9e-12

Table S166.  Gene #75: 'Del Peak 47(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
DEL PEAK 47(22Q13.32) MUTATED 108 45 28 23
DEL PEAK 47(22Q13.32) WILD-TYPE 92 189 72 18

Figure S166.  Get High-res Image Gene #75: 'Del Peak 47(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 575

  • Number of copy number variation regions = 75

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Chi-square test

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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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