Lung 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 82 peak regions and 10 molecular subtypes across 472 patients, 291 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1p34.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 2(1p22.3) cnvs correlated to 'CN_CNMF'.

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

  • Amp Peak 4(3q26.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 5(4q12) cnvs correlated to 'CN_CNMF'.

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

  • Amp Peak 7(5p13.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Amp Peak 8(5q35.1) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 9(6p21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 10(7p21.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 11(7p11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 12(7q31.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 13(8p11.23) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 14(8p11.21) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Amp Peak 15(8q11.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 16(8q24.21) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 17(10p15.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 18(11q13.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 19(12p12.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 20(12q14.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 21(12q15) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 23(14q13.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 24(17q12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 25(17q23.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 26(18q11.2) cnvs correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 28(20p11.21) cnvs correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 29(20q13.33) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 31(Xq28) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

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

  • Del Peak 5(2q37.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 6(3p21.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 8(3q29) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 9(4p16.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 10(4q22.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 11(4q35.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 13(5q22.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 15(6q22.31) cnvs correlated to 'METHLYATION_CNMF'.

  • Del Peak 16(6q26) cnvs correlated to 'METHLYATION_CNMF'.

  • Del Peak 17(8p23.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 18(8p12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 19(8p11.21) cnvs correlated to 'CN_CNMF'.

  • Del Peak 21(9p23) cnvs correlated to 'CN_CNMF'.

  • Del Peak 22(9p21.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 23(9q21.11) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 25(10q26.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

  • Del Peak 28(11q25) cnvs correlated to 'MRNASEQ_CNMF'.

  • Del Peak 29(12p13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 30(12q12) cnvs correlated to 'CN_CNMF'.

  • Del Peak 31(12q24.33) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 32(13q12.11) cnvs correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 33(13q12.13) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 34(13q14.2) cnvs correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 35(13q34) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 36(14q32.33) cnvs correlated to 'CN_CNMF'.

  • Del Peak 37(15q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 38(16q23.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 39(16q24.3) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 40(17p13.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 41(18q21.32) cnvs correlated to 'CN_CNMF'.

  • Del Peak 42(18q23) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 43(19p13.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 44(19p13.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 45(19p12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 46(19q13.33) cnvs correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 47(20p13) cnvs correlated to 'CN_CNMF'.

  • Del Peak 48(21q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 49(21q21.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 50(22q13.32) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 51(Xp22.2) 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 82 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 291 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 Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
Del Peak 10(4q22 1) 142 (30%) 330 0.000214
(0.117) 		9.89e-05
(0.0561) 		3.67e-07
(0.000256) 		9.89e-08
(7.18e-05) 		0.151
(1.00) 		0.0286
(1.00) 		5.41e-07
(0.000372) 		3.52e-12
(2.78e-09) 		5.18e-07
(0.000357) 		1.14e-08
(8.59e-06)
Amp Peak 4(3q26 2) 157 (33%) 315 0.000264
(0.142) 		0.00332
(1.00) 		5.01e-10
(3.89e-07) 		5.52e-08
(4.06e-05) 		0.000631
(0.329) 		0.00307
(1.00) 		1.11e-08
(8.4e-06) 		3.47e-07
(0.000243) 		8.66e-08
(6.31e-05) 		9.8e-08
(7.12e-05)
Amp Peak 11(7p11 2) 252 (53%) 220 1
(1.00) 		1
(1.00) 		1.27e-18
(1.02e-15) 		2e-05
(0.0118) 		0.00114
(0.568) 		0.000263
(0.142) 		2.09e-11
(1.64e-08) 		1.36e-09
(1.05e-06) 		1.72e-06
(0.00113) 		4.75e-07
(0.000329)
Amp Peak 24(17q12) 208 (44%) 264 0.179
(1.00) 		0.049
(1.00) 		6.08e-14
(4.86e-11) 		8.27e-07
(0.000562) 		0.0638
(1.00) 		0.00016
(0.0888) 		1.05e-06
(0.000706) 		6.71e-08
(4.93e-05) 		3.19e-06
(0.00207) 		1.01e-07
(7.3e-05)
Amp Peak 25(17q23 1) 230 (49%) 242 0.081
(1.00) 		0.208
(1.00) 		2.25e-14
(1.81e-11) 		2.11e-08
(1.58e-05) 		0.00156
(0.758) 		4.12e-07
(0.000287) 		1.84e-07
(0.000132) 		2.9e-10
(2.26e-07) 		1.71e-05
(0.0102) 		5.39e-06
(0.00341)
Del Peak 11(4q35 1) 172 (36%) 300 0.00204
(0.964) 		0.00118
(0.588) 		7.48e-10
(5.8e-07) 		1.36e-11
(1.07e-08) 		0.0381
(1.00) 		0.000196
(0.108) 		2.07e-11
(1.63e-08) 		7.71e-17
(6.21e-14) 		1.07e-08
(8.08e-06) 		1.67e-14
(1.34e-11)
Del Peak 33(13q12 13) 266 (56%) 206 0.00862
(1.00) 		0.0218
(1.00) 		1.05e-19
(8.48e-17) 		0.000107
(0.0607) 		0.000524
(0.276) 		6.68e-07
(0.000457) 		4.8e-06
(0.00306) 		8.61e-09
(6.53e-06) 		3.21e-05
(0.0188) 		3.52e-06
(0.00227)
Amp Peak 10(7p21 1) 261 (55%) 211 0.743
(1.00) 		1
(1.00) 		6.95e-20
(5.65e-17) 		4.93e-06
(0.00313) 		0.00184
(0.884) 		0.00104
(0.523) 		7.98e-08
(5.83e-05) 		2.31e-08
(1.73e-05) 		0.00021
(0.115) 		0.000238
(0.129)
Amp Peak 15(8q11 1) 214 (45%) 258 0.00472
(1.00) 		0.0134
(1.00) 		3.04e-22
(2.49e-19) 		1.14e-07
(8.2e-05) 		0.0344
(1.00) 		0.00467
(1.00) 		4.21e-06
(0.0027) 		2.93e-05
(0.0173) 		3.26e-07
(0.000228) 		4.91e-06
(0.00312)
Amp Peak 16(8q24 21) 298 (63%) 174 0.0343
(1.00) 		0.0341
(1.00) 		8.4e-20
(6.82e-17) 		3.72e-08
(2.76e-05) 		0.157
(1.00) 		0.00162
(0.781) 		3.06e-07
(0.000215) 		1.37e-05
(0.00824) 		1.15e-05
(0.00703) 		1.73e-05
(0.0104)
Amp Peak 18(11q13 3) 157 (33%) 315 0.00118
(0.588) 		0.000736
(0.377) 		5.94e-14
(4.76e-11) 		1.94e-05
(0.0116) 		0.0127
(1.00) 		0.00689
(1.00) 		3.18e-05
(0.0186) 		3.55e-07
(0.000248) 		4.77e-08
(3.52e-05) 		8.56e-08
(6.25e-05)
Amp Peak 19(12p12 1) 163 (35%) 309 0.198
(1.00) 		0.033
(1.00) 		5.45e-22
(4.46e-19) 		4.14e-06
(0.00266) 		0.0345
(1.00) 		0.0834
(1.00) 		9.69e-07
(0.000652) 		3.96e-06
(0.00255) 		1.04e-05
(0.00637) 		7.46e-06
(0.00465)
Amp Peak 20(12q14 1) 148 (31%) 324 0.406
(1.00) 		0.302
(1.00) 		2.65e-24
(2.17e-21) 		1.45e-07
(0.000104) 		0.0215
(1.00) 		0.00722
(1.00) 		2.68e-07
(0.000189) 		2.26e-09
(1.73e-06) 		2.63e-08
(1.96e-05) 		9.79e-09
(7.41e-06)
Amp Peak 21(12q15) 151 (32%) 321 0.221
(1.00) 		0.103
(1.00) 		1.49e-21
(1.22e-18) 		2.35e-08
(1.76e-05) 		0.0146
(1.00) 		0.00471
(1.00) 		4.86e-07
(0.000336) 		2.18e-07
(0.000155) 		1.92e-07
(0.000137) 		3.98e-09
(3.04e-06)
Amp Peak 23(14q13 3) 211 (45%) 261 0.562
(1.00) 		0.254
(1.00) 		2.03e-11
(1.6e-08) 		4.73e-06
(0.00302) 		0.00213
(1.00) 		0.0122
(1.00) 		2.55e-10
(1.98e-07) 		5.25e-05
(0.0303) 		2.37e-06
(0.00155) 		3.6e-09
(2.76e-06)
Del Peak 9(4p16 3) 116 (25%) 356 0.595
(1.00) 		0.453
(1.00) 		1.56e-05
(0.00939) 		2.31e-05
(0.0136) 		0.0232
(1.00) 		0.0499
(1.00) 		9.45e-07
(0.000637) 		3.34e-07
(0.000234) 		6.15e-07
(0.000421) 		4.73e-08
(3.49e-05)
Del Peak 12(5q11 2) 166 (35%) 306 0.26
(1.00) 		0.254
(1.00) 		1.9e-12
(1.51e-09) 		2.02e-07
(0.000144) 		0.00426
(1.00) 		0.0113
(1.00) 		1.01e-05
(0.0062) 		7.77e-08
(5.69e-05) 		4.54e-07
(0.000316) 		7.44e-08
(5.46e-05)
Del Peak 13(5q22 1) 189 (40%) 283 0.0447
(1.00) 		0.0515
(1.00) 		1.08e-12
(8.59e-10) 		2.56e-08
(1.91e-05) 		0.0017
(0.817) 		0.00377
(1.00) 		6.18e-07
(0.000423) 		2.49e-08
(1.86e-05) 		1.2e-09
(9.24e-07) 		1.45e-09
(1.12e-06)
Del Peak 17(8p23 2) 229 (49%) 243 0.00526
(1.00) 		0.00382
(1.00) 		7.67e-17
(6.19e-14) 		9.17e-05
(0.0522) 		0.018
(1.00) 		0.000354
(0.188) 		1.05e-05
(0.00644) 		1.83e-07
(0.000131) 		0.00425
(1.00) 		1.67e-06
(0.0011)
Del Peak 32(13q12 11) 265 (56%) 207 0.00113
(0.567) 		0.0134
(1.00) 		1.38e-19
(1.12e-16) 		0.000608
(0.319) 		0.00188
(0.898) 		1.49e-06
(0.000985) 		2.36e-06
(0.00154) 		3.99e-09
(3.05e-06) 		7.35e-06
(0.0046) 		8.66e-07
(0.000586)
Del Peak 34(13q14 2) 256 (54%) 216 0.00862
(1.00) 		0.0218
(1.00) 		7.61e-22
(6.22e-19) 		0.000783
(0.399) 		0.000647
(0.336) 		1.04e-05
(0.00639) 		8.81e-07
(0.000595) 		4.07e-08
(3.01e-05) 		3.24e-05
(0.0189) 		1.26e-06
(0.000844)
Del Peak 37(15q11 2) 239 (51%) 233 0.168
(1.00) 		0.157
(1.00) 		1.81e-10
(1.41e-07) 		0.000193
(0.106) 		0.0928
(1.00) 		0.000161
(0.0895) 		1.83e-09
(1.41e-06) 		1.05e-07
(7.6e-05) 		0.00188
(0.896) 		0.000156
(0.0872)
Del Peak 43(19p13 3) 252 (53%) 220 0.572
(1.00) 		0.665
(1.00) 		2.6e-12
(2.05e-09) 		2.35e-07
(0.000167) 		0.564
(1.00) 		0.306
(1.00) 		2.15e-06
(0.00141) 		1.9e-08
(1.43e-05) 		2.4e-06
(0.00156) 		9.36e-06
(0.00579)
Del Peak 44(19p13 2) 246 (52%) 226 0.694
(1.00) 		1
(1.00) 		1.25e-11
(9.88e-09) 		2.22e-08
(1.66e-05) 		0.378
(1.00) 		0.187
(1.00) 		1.06e-06
(0.000713) 		1.28e-06
(0.000854) 		1.47e-06
(0.000977) 		4.99e-07
(0.000344)
Del Peak 45(19p12) 199 (42%) 273 0.519
(1.00) 		0.658
(1.00) 		9.72e-13
(7.73e-10) 		1.71e-05
(0.0102) 		0.603
(1.00) 		0.266
(1.00) 		8.24e-05
(0.0471) 		5.88e-06
(0.00369) 		2.34e-05
(0.0138) 		0.0002
(0.11)
Del Peak 48(21q11 2) 157 (33%) 315 0.0604
(1.00) 		0.0501
(1.00) 		3.1e-11
(2.43e-08) 		0.000131
(0.0735) 		0.00624
(1.00) 		0.00469
(1.00) 		8.83e-08
(6.43e-05) 		4.62e-09
(3.52e-06) 		1.98e-05
(0.0118) 		5.83e-06
(0.00367)
Del Peak 49(21q21 3) 153 (32%) 319 0.0288
(1.00) 		0.033
(1.00) 		9.45e-11
(7.39e-08) 		1.28e-05
(0.00777) 		0.000525
(0.276) 		0.00065
(0.338) 		1.19e-10
(9.28e-08) 		2.08e-12
(1.65e-09) 		2.98e-05
(0.0175) 		8.38e-07
(0.000568)
Del Peak 50(22q13 32) 224 (47%) 248 0.0692
(1.00) 		0.0871
(1.00) 		6.18e-13
(4.92e-10) 		4.57e-08
(3.38e-05) 		0.00863
(1.00) 		0.0171
(1.00) 		5.08e-09
(3.86e-06) 		4.88e-09
(3.71e-06) 		1.67e-05
(0.01) 		3.76e-08
(2.79e-05)
Amp Peak 14(8p11 21) 162 (34%) 310 0.253
(1.00) 		0.124
(1.00) 		3.42e-21
(2.78e-18) 		0.000128
(0.0719) 		0.0149
(1.00) 		0.00534
(1.00) 		4.59e-07
(0.000319) 		2.54e-07
(0.00018) 		3.74e-05
(0.0218) 		0.000487
(0.258)
Amp Peak 17(10p15 1) 124 (26%) 348 0.023
(1.00) 		0.0262
(1.00) 		4.17e-06
(0.00267) 		2.59e-07
(0.000183) 		0.00434
(1.00) 		0.0346
(1.00) 		0.00022
(0.12) 		2.26e-06
(0.00148) 		0.000724
(0.372) 		0.000175
(0.097)
Amp Peak 27(19q12) 126 (27%) 346 0.0514
(1.00) 		0.0219
(1.00) 		1.29e-08
(9.68e-06) 		0.000304
(0.163) 		0.0685
(1.00) 		0.0791
(1.00) 		0.00105
(0.526) 		4.57e-05
(0.0265) 		1.36e-06
(0.000904) 		5.18e-07
(0.000357)
Del Peak 1(1p36 13) 108 (23%) 364 0.795
(1.00) 		0.441
(1.00) 		1.59e-06
(0.00105) 		2.18e-05
(0.0129) 		0.437
(1.00) 		0.363
(1.00) 		5.33e-05
(0.0308) 		0.000179
(0.0991) 		0.000215
(0.118) 		0.00724
(1.00)
Del Peak 6(3p21 31) 227 (48%) 245 0.132
(1.00) 		0.478
(1.00) 		7.53e-06
(0.00469) 		3.21e-06
(0.00208) 		0.0411
(1.00) 		0.00737
(1.00) 		0.0189
(1.00) 		3.35e-09
(2.57e-06) 		8.43e-06
(0.00522) 		3e-06
(0.00195)
Del Peak 18(8p12) 205 (43%) 267 0.106
(1.00) 		0.12
(1.00) 		1.83e-15
(1.47e-12) 		1.95e-05
(0.0116) 		0.0424
(1.00) 		0.0222
(1.00) 		0.000262
(0.141) 		7.86e-06
(0.00488) 		0.00424
(1.00) 		7.8e-06
(0.00485)
Amp Peak 12(7q31 2) 200 (42%) 272 0.482
(1.00) 		0.429
(1.00) 		2.86e-09
(2.19e-06) 		5.48e-05
(0.0315) 		0.206
(1.00) 		0.052
(1.00) 		1.03e-09
(7.94e-07) 		1.03e-07
(7.46e-05) 		0.00659
(1.00) 		0.00076
(0.388)
Amp Peak 13(8p11 23) 126 (27%) 346 0.294
(1.00) 		0.107
(1.00) 		2.17e-16
(1.75e-13) 		8.25e-06
(0.00512) 		0.0844
(1.00) 		0.0267
(1.00) 		0.000334
(0.178) 		1.93e-05
(0.0116) 		0.00646
(1.00) 		0.012
(1.00)
Amp Peak 29(20q13 33) 225 (48%) 247 0.00559
(1.00) 		0.0301
(1.00) 		1.03e-07
(7.46e-05) 		0.00296
(1.00) 		0.00426
(1.00) 		0.00335
(1.00) 		1.15e-05
(0.00701) 		0.00467
(1.00) 		1.02e-05
(0.00627) 		1.34e-05
(0.00808)
Del Peak 23(9q21 11) 231 (49%) 241 0.0335
(1.00) 		0.597
(1.00) 		1.49e-07
(0.000107) 		5.08e-05
(0.0294) 		0.0726
(1.00) 		0.0112
(1.00) 		0.00567
(1.00) 		9.41e-06
(0.00581) 		0.00495
(1.00) 		1.2e-05
(0.00728)
Del Peak 35(13q34) 217 (46%) 255 0.0356
(1.00) 		0.0445
(1.00) 		2.2e-15
(1.77e-12) 		0.0508
(1.00) 		0.00359
(1.00) 		0.00079
(0.402) 		3.88e-05
(0.0226) 		5.1e-06
(0.00323) 		0.00145
(0.705) 		0.000248
(0.134)
Del Peak 38(16q23 1) 160 (34%) 312 0.0587
(1.00) 		0.312
(1.00) 		2.59e-07
(0.000183) 		0.00046
(0.244) 		0.000698
(0.36) 		0.0174
(1.00) 		2.74e-07
(0.000193) 		3.66e-08
(2.72e-05) 		0.00644
(1.00) 		0.00396
(1.00)
Del Peak 40(17p13 3) 252 (53%) 220 0.386
(1.00) 		0.609
(1.00) 		2.78e-13
(2.22e-10) 		7.56e-08
(5.54e-05) 		0.0334
(1.00) 		0.00158
(0.765) 		6.83e-05
(0.0392) 		6.38e-06
(0.004) 		0.00541
(1.00) 		0.00352
(1.00)
Amp Peak 3(1q21 3) 336 (71%) 136 0.362
(1.00) 		0.465
(1.00) 		5.64e-06
(0.00356) 		8.32e-07
(0.000565) 		0.458
(1.00) 		0.357
(1.00) 		0.203
(1.00) 		0.866
(1.00) 		0.0202
(1.00) 		0.000116
(0.0658)
Amp Peak 28(20p11 21) 179 (38%) 293 0.0611
(1.00) 		0.0953
(1.00) 		1.1e-05
(0.00673) 		0.00708
(1.00) 		0.338
(1.00) 		0.0379
(1.00) 		0.00294
(1.00) 		0.00475
(1.00) 		0.000234
(0.127) 		3.44e-05
(0.0201)
Amp Peak 31(Xq28) 151 (32%) 321 0.301
(1.00) 		0.123
(1.00) 		3.01e-10
(2.34e-07) 		5.94e-05
(0.0341) 		0.0244
(1.00) 		0.0308
(1.00) 		0.000272
(0.146) 		0.00287
(1.00) 		0.0264
(1.00) 		0.0338
(1.00)
Del Peak 39(16q24 3) 178 (38%) 294 0.16
(1.00) 		0.631
(1.00) 		1.66e-06
(0.0011) 		0.00282
(1.00) 		0.0186
(1.00) 		0.08
(1.00) 		2.12e-06
(0.00139) 		3.23e-06
(0.00209) 		0.0184
(1.00) 		0.00509
(1.00)
Del Peak 46(19q13 33) 174 (37%) 298 0.272
(1.00) 		0.383
(1.00) 		2.02e-07
(0.000144) 		0.00292
(1.00) 		0.0819
(1.00) 		0.208
(1.00) 		0.0782
(1.00) 		0.00945
(1.00) 		0.000137
(0.0767) 		1.17e-05
(0.00712)
Amp Peak 6(5p15 33) 304 (64%) 168 0.878
(1.00) 		0.901
(1.00) 		2.75e-21
(2.24e-18) 		0.0397
(1.00) 		0.0565
(1.00) 		0.000798
(0.405) 		1.29e-07
(9.29e-05) 		0.00324
(1.00) 		0.00357
(1.00) 		0.00213
(1.00)
Amp Peak 7(5p13 1) 280 (59%) 192 0.263
(1.00) 		0.897
(1.00) 		5.67e-18
(4.58e-15) 		0.0135
(1.00) 		0.443
(1.00) 		0.0187
(1.00) 		6.76e-07
(0.000461) 		0.074
(1.00) 		0.0016
(0.773) 		0.0055
(1.00)
Amp Peak 8(5q35 1) 110 (23%) 362 0.0862
(1.00) 		0.453
(1.00) 		0.00391
(1.00) 		8.8e-07
(0.000595) 		0.0909
(1.00) 		0.2
(1.00) 		0.0014
(0.683) 		0.000153
(0.0858) 		0.00108
(0.543) 		0.0233
(1.00)
Amp Peak 9(6p21 1) 173 (37%) 299 0.675
(1.00) 		0.206
(1.00) 		0.000168
(0.0934) 		1.05e-07
(7.55e-05) 		0.081
(1.00) 		0.609
(1.00) 		0.0298
(1.00) 		0.94
(1.00) 		0.15
(1.00) 		0.0242
(1.00)
Amp Peak 26(18q11 2) 94 (20%) 378 0.195
(1.00) 		0.0151
(1.00) 		0.000918
(0.464) 		1.07e-08
(8.08e-06) 		0.0431
(1.00) 		0.000816
(0.414) 		0.0121
(1.00) 		0.00315
(1.00) 		0.00265
(1.00) 		1.45e-06
(0.000961)
Del Peak 2(1p13 3) 139 (29%) 333 0.844
(1.00) 		0.896
(1.00) 		9.97e-07
(0.00067) 		9.81e-05
(0.0557) 		0.626
(1.00) 		0.717
(1.00) 		0.000581
(0.305) 		0.00557
(1.00) 		0.0353
(1.00) 		0.0304
(1.00)
Del Peak 3(1p13 1) 137 (29%) 335 0.703
(1.00) 		0.707
(1.00) 		1.93e-06
(0.00127) 		2.2e-05
(0.013) 		0.124
(1.00) 		0.535
(1.00) 		0.00121
(0.601) 		0.0066
(1.00) 		0.0187
(1.00) 		0.0288
(1.00)
Del Peak 8(3q29) 129 (27%) 343 0.71
(1.00) 		0.602
(1.00) 		0.145
(1.00) 		8.11e-05
(0.0465) 		0.00515
(1.00) 		0.0168
(1.00) 		8.83e-05
(0.0503) 		0.0732
(1.00) 		0.637
(1.00) 		0.0249
(1.00)
Del Peak 25(10q26 3) 130 (28%) 342 0.748
(1.00) 		0.283
(1.00) 		4.78e-06
(0.00305) 		0.000256
(0.138) 		0.00268
(1.00) 		0.0237
(1.00) 		0.000653
(0.338) 		0.0171
(1.00) 		0.0196
(1.00) 		0.00601
(1.00)
Del Peak 26(11p15 5) 126 (27%) 346 0.268
(1.00) 		0.0576
(1.00) 		4.04e-06
(0.00259) 		0.012
(1.00) 		0.00767
(1.00) 		0.00204
(0.964) 		0.00463
(1.00) 		5.3e-06
(0.00335) 		0.00773
(1.00) 		0.00215
(1.00)
Del Peak 29(12p13 2) 126 (27%) 346 0.255
(1.00) 		0.719
(1.00) 		0.000172
(0.0952) 		7.21e-07
(0.000491) 		0.0774
(1.00) 		0.021
(1.00) 		0.0241
(1.00) 		0.0928
(1.00) 		0.987
(1.00) 		0.968
(1.00)
Del Peak 31(12q24 33) 115 (24%) 357 0.063
(1.00) 		0.0396
(1.00) 		6.54e-06
(0.00409) 		0.00195
(0.928) 		0.0223
(1.00) 		0.00328
(1.00) 		0.00995
(1.00) 		0.00104
(0.523) 		0.00405
(1.00) 		5.84e-06
(0.00367)
Del Peak 42(18q23) 228 (48%) 244 0.029
(1.00) 		0.0968
(1.00) 		9.31e-13
(7.41e-10) 		0.0205
(1.00) 		0.00395
(1.00) 		0.00135
(0.663) 		0.00038
(0.202) 		0.000628
(0.328) 		0.0133
(1.00) 		0.00274
(1.00)
Amp Peak 1(1p34 3) 125 (26%) 347 0.553
(1.00) 		0.384
(1.00) 		5.41e-07
(0.000372) 		0.00816
(1.00) 		0.169
(1.00) 		0.243
(1.00) 		0.0237
(1.00) 		0.0591
(1.00) 		0.241
(1.00) 		0.708
(1.00)
Amp Peak 2(1p22 3) 124 (26%) 348 0.876
(1.00) 		1
(1.00) 		4.8e-07
(0.000332) 		0.00253
(1.00) 		0.183
(1.00) 		0.399
(1.00) 		0.0527
(1.00) 		0.00703
(1.00) 		0.434
(1.00) 		0.108
(1.00)
Amp Peak 5(4q12) 88 (19%) 384 0.703
(1.00) 		0.206
(1.00) 		6.06e-09
(4.6e-06) 		0.0314
(1.00) 		0.0221
(1.00) 		0.0265
(1.00) 		0.0725
(1.00) 		0.00728
(1.00) 		0.0228
(1.00) 		0.00489
(1.00)
Del Peak 5(2q37 3) 63 (13%) 409 0.703
(1.00) 		0.206
(1.00) 		0.00033
(0.177) 		0.0016
(0.773) 		0.22
(1.00) 		0.151
(1.00) 		0.0125
(1.00) 		0.00267
(1.00) 		0.00448
(1.00) 		0.0013
(0.639)
Del Peak 15(6q22 31) 234 (50%) 238 0.54
(1.00) 		0.187
(1.00) 		0.022
(1.00) 		1.29e-06
(0.000861) 		0.308
(1.00) 		0.0544
(1.00) 		0.055
(1.00) 		0.981
(1.00) 		0.374
(1.00) 		0.527
(1.00)
Del Peak 16(6q26) 238 (50%) 234 0.368
(1.00) 		0.276
(1.00) 		0.0119
(1.00) 		8.64e-05
(0.0494) 		0.168
(1.00) 		0.00944
(1.00) 		0.226
(1.00) 		0.635
(1.00) 		0.18
(1.00) 		0.106
(1.00)
Del Peak 19(8p11 21) 107 (23%) 365 0.795
(1.00) 		0.504
(1.00) 		2.79e-11
(2.19e-08) 		0.018
(1.00) 		0.721
(1.00) 		0.318
(1.00) 		0.234
(1.00) 		0.101
(1.00) 		0.34
(1.00) 		0.0413
(1.00)
Del Peak 21(9p23) 258 (55%) 214 0.521
(1.00) 		0.901
(1.00) 		3.22e-07
(0.000226) 		0.582
(1.00) 		0.62
(1.00) 		0.598
(1.00) 		0.0572
(1.00) 		0.0222
(1.00) 		0.469
(1.00) 		0.153
(1.00)
Del Peak 22(9p21 3) 264 (56%) 208 0.521
(1.00) 		0.901
(1.00) 		1.79e-06
(0.00118) 		0.521
(1.00) 		0.328
(1.00) 		0.288
(1.00) 		0.00457
(1.00) 		0.013
(1.00) 		0.826
(1.00) 		0.204
(1.00)
Del Peak 27(11q23 2) 109 (23%) 363 0.433
(1.00) 		0.453
(1.00) 		0.000122
(0.0686) 		0.0184
(1.00) 		0.009
(1.00) 		0.00266
(1.00) 		0.000518
(0.273) 		0.00198
(0.938) 		0.0165
(1.00) 		0.13
(1.00)
Del Peak 28(11q25) 105 (22%) 367 0.108
(1.00) 		0.0799
(1.00) 		0.00149
(0.724) 		0.0454
(1.00) 		0.0012
(0.597) 		0.00644
(1.00) 		0.000464
(0.246) 		0.00596
(1.00) 		0.114
(1.00) 		0.433
(1.00)
Del Peak 30(12q12) 90 (19%) 382 0.597
(1.00) 		0.644
(1.00) 		1.19e-05
(0.00724) 		0.021
(1.00) 		0.107
(1.00) 		0.0158
(1.00) 		0.0399
(1.00) 		0.184
(1.00) 		0.199
(1.00) 		0.0222
(1.00)
Del Peak 36(14q32 33) 140 (30%) 332 0.703
(1.00) 		0.302
(1.00) 		0.000135
(0.0757) 		0.521
(1.00) 		0.16
(1.00) 		0.0627
(1.00) 		0.389
(1.00) 		0.0751
(1.00) 		0.0197
(1.00) 		0.186
(1.00)
Del Peak 41(18q21 32) 233 (49%) 239 0.115
(1.00) 		0.227
(1.00) 		8.58e-10
(6.64e-07) 		0.0508
(1.00) 		0.00133
(0.652) 		0.0023
(1.00) 		0.00455
(1.00) 		0.0109
(1.00) 		0.0409
(1.00) 		0.0217
(1.00)
Del Peak 47(20p13) 121 (26%) 351 0.105
(1.00) 		0.268
(1.00) 		2.4e-06
(0.00156) 		0.000655
(0.339) 		0.00552
(1.00) 		0.00106
(0.534) 		0.0146
(1.00) 		0.0135
(1.00) 		0.722
(1.00) 		0.689
(1.00)
Del Peak 51(Xp22 2) 137 (29%) 335 0.691
(1.00) 		0.896
(1.00) 		1.99e-07
(0.000142) 		0.00131
(0.644) 		0.0885
(1.00) 		0.0284
(1.00) 		0.000668
(0.344) 		0.00124
(0.612) 		0.544
(1.00) 		0.514
(1.00)
Amp Peak 22(13q33 3) 72 (15%) 400 0.172
(1.00) 		0.105
(1.00) 		0.433
(1.00) 		0.00285
(1.00) 		0.663
(1.00) 		0.298
(1.00) 		0.917
(1.00) 		0.267
(1.00) 		0.27
(1.00) 		0.0982
(1.00)
Amp Peak 30(22q11 22) 81 (17%) 391 0.268
(1.00) 		0.162
(1.00) 		0.0014
(0.684) 		0.601
(1.00) 		0.0232
(1.00) 		0.119
(1.00) 		0.474
(1.00) 		0.222
(1.00) 		0.0605
(1.00) 		0.0982
(1.00)
Del Peak 4(2q22 1) 47 (10%) 425 0.869
(1.00) 		0.78
(1.00) 		0.00238
(1.00) 		0.0379
(1.00) 		0.0306
(1.00) 		0.471
(1.00) 		0.0542
(1.00) 		0.00242
(1.00) 		0.0476
(1.00) 		0.121
(1.00)
Del Peak 7(3q11 1) 133 (28%) 339 0.609
(1.00) 		0.602
(1.00) 		0.0414
(1.00) 		0.0274
(1.00) 		0.366
(1.00) 		0.298
(1.00) 		0.168
(1.00) 		0.0277
(1.00) 		0.856
(1.00) 		0.728
(1.00)
Del Peak 14(6q12) 158 (33%) 314 0.532
(1.00) 		1
(1.00) 		0.0598
(1.00) 		0.0244
(1.00) 		0.243
(1.00) 		0.159
(1.00) 		0.882
(1.00) 		0.928
(1.00) 		0.172
(1.00) 		0.005
(1.00)
Del Peak 20(8q11 21) 59 (12%) 413 1
(1.00) 		1
(1.00) 		0.796
(1.00) 		0.0628
(1.00) 		0.537
(1.00) 		0.676
(1.00) 		0.861
(1.00) 		0.488
(1.00) 		0.26
(1.00) 		0.183
(1.00)
Del Peak 24(10p15 3) 113 (24%) 359 1
(1.00) 		1
(1.00) 		0.000735
(0.377) 		0.000614
(0.321) 		0.504
(1.00) 		0.56
(1.00) 		0.00438
(1.00) 		0.476
(1.00) 		0.002
(0.949) 		0.0227
(1.00)
'Amp Peak 1(1p34.3) mutation analysis' versus 'CN_CNMF'

P value = 5.41e-07 (Fisher's exact test), Q value = 0.00037

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 1(1P34.3) MUTATED 64 33 21 7
AMP PEAK 1(1P34.3) WILD-TYPE 84 155 66 42

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

'Amp Peak 2(1p22.3) mutation analysis' versus 'CN_CNMF'

P value = 4.8e-07 (Fisher's exact test), Q value = 0.00033

Table S2.  Gene #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 2(1P22.3) MUTATED 64 31 20 9
AMP PEAK 2(1P22.3) WILD-TYPE 84 157 67 40

Figure S2.  Get High-res Image Gene #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 5.64e-06 (Fisher's exact test), Q value = 0.0036

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 3(1Q21.3) MUTATED 118 110 65 43
AMP PEAK 3(1Q21.3) WILD-TYPE 30 78 22 6

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

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

P value = 8.32e-07 (Chi-square test), Q value = 0.00056

Table S4.  Gene #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 3(1Q21.3) MUTATED 63 82 70 52 22
AMP PEAK 3(1Q21.3) WILD-TYPE 27 12 25 48 3

Figure S4.  Get High-res Image Gene #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 0.000116 (Fisher's exact test), Q value = 0.066

Table S5.  Gene #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 3(1Q21.3) MUTATED 111 69 101
AMP PEAK 3(1Q21.3) WILD-TYPE 52 46 19

Figure S5.  Get High-res Image Gene #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 4(3q26.2) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000264 (Fisher's exact test), Q value = 0.14

Table S6.  Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
AMP PEAK 4(3Q26.2) MUTATED 0 6 0 4
AMP PEAK 4(3Q26.2) WILD-TYPE 5 3 12 2

Figure S6.  Get High-res Image Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 4(3q26.2) mutation analysis' versus 'CN_CNMF'

P value = 5.01e-10 (Fisher's exact test), Q value = 3.9e-07

Table S7.  Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 4(3Q26.2) MUTATED 52 35 52 18
AMP PEAK 4(3Q26.2) WILD-TYPE 96 153 35 31

Figure S7.  Get High-res Image Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 4(3q26.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.52e-08 (Chi-square test), Q value = 4.1e-05

Table S8.  Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 4(3Q26.2) MUTATED 7 43 31 36 14
AMP PEAK 4(3Q26.2) WILD-TYPE 83 51 64 64 11

Figure S8.  Get High-res Image Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 4(3q26.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.11e-08 (Chi-square test), Q value = 8.4e-06

Table S9.  Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 4(3Q26.2) MUTATED 40 4 25 42 17
AMP PEAK 4(3Q26.2) WILD-TYPE 58 71 29 39 27

Figure S9.  Get High-res Image Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 4(3q26.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.47e-07 (Fisher's exact test), Q value = 0.00024

Table S10.  Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 4(3Q26.2) MUTATED 32 55 41
AMP PEAK 4(3Q26.2) WILD-TYPE 120 50 54

Figure S10.  Get High-res Image Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 4(3q26.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.66e-08 (Fisher's exact test), Q value = 6.3e-05

Table S11.  Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 4(3Q26.2) MUTATED 32 90 17
AMP PEAK 4(3Q26.2) WILD-TYPE 126 93 40

Figure S11.  Get High-res Image Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 4(3q26.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.8e-08 (Fisher's exact test), Q value = 7.1e-05

Table S12.  Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 4(3Q26.2) MUTATED 32 46 61
AMP PEAK 4(3Q26.2) WILD-TYPE 131 69 59

Figure S12.  Get High-res Image Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 5(4q12) mutation analysis' versus 'CN_CNMF'

P value = 6.06e-09 (Fisher's exact test), Q value = 4.6e-06

Table S13.  Gene #5: 'Amp Peak 5(4q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 5(4Q12) MUTATED 45 13 25 5
AMP PEAK 5(4Q12) WILD-TYPE 103 175 62 44

Figure S13.  Get High-res Image Gene #5: 'Amp Peak 5(4q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.75e-21 (Fisher's exact test), Q value = 2.2e-18

Table S14.  Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 6(5P15.33) MUTATED 136 83 48 37
AMP PEAK 6(5P15.33) WILD-TYPE 12 105 39 12

Figure S14.  Get High-res Image Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.29e-07 (Chi-square test), Q value = 9.3e-05

Table S15.  Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 6(5P15.33) MUTATED 80 41 19 55 32
AMP PEAK 6(5P15.33) WILD-TYPE 18 34 35 26 12

Figure S15.  Get High-res Image Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 7(5p13.1) mutation analysis' versus 'CN_CNMF'

P value = 5.67e-18 (Fisher's exact test), Q value = 4.6e-15

Table S16.  Gene #7: 'Amp Peak 7(5p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 7(5P13.1) MUTATED 124 75 42 39
AMP PEAK 7(5P13.1) WILD-TYPE 24 113 45 10

Figure S16.  Get High-res Image Gene #7: 'Amp Peak 7(5p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 7(5p13.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.76e-07 (Chi-square test), Q value = 0.00046

Table S17.  Gene #7: 'Amp Peak 7(5p13.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 7(5P13.1) MUTATED 69 36 15 56 28
AMP PEAK 7(5P13.1) WILD-TYPE 29 39 39 25 16

Figure S17.  Get High-res Image Gene #7: 'Amp Peak 7(5p13.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 8(5q35.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.8e-07 (Chi-square test), Q value = 0.00059

Table S18.  Gene #8: 'Amp Peak 8(5q35.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 8(5Q35.1) MUTATED 41 14 16 17 8
AMP PEAK 8(5Q35.1) WILD-TYPE 49 80 79 83 17

Figure S18.  Get High-res Image Gene #8: 'Amp Peak 8(5q35.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 8(5q35.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.086

Table S19.  Gene #8: 'Amp Peak 8(5q35.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 8(5Q35.1) MUTATED 49 11 24
AMP PEAK 8(5Q35.1) WILD-TYPE 103 94 71

Figure S19.  Get High-res Image Gene #8: 'Amp Peak 8(5q35.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 9(6p21.1) mutation analysis' versus 'CN_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.093

Table S20.  Gene #9: 'Amp Peak 9(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 9(6P21.1) MUTATED 62 49 34 28
AMP PEAK 9(6P21.1) WILD-TYPE 86 139 53 21

Figure S20.  Get High-res Image Gene #9: 'Amp Peak 9(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 9(6p21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.05e-07 (Chi-square test), Q value = 7.6e-05

Table S21.  Gene #9: 'Amp Peak 9(6p21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 9(6P21.1) MUTATED 31 54 34 17 14
AMP PEAK 9(6P21.1) WILD-TYPE 59 40 61 83 11

Figure S21.  Get High-res Image Gene #9: 'Amp Peak 9(6p21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 10(7p21.1) mutation analysis' versus 'CN_CNMF'

P value = 6.95e-20 (Fisher's exact test), Q value = 5.6e-17

Table S22.  Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 10(7P21.1) MUTATED 125 70 50 16
AMP PEAK 10(7P21.1) WILD-TYPE 23 118 37 33

Figure S22.  Get High-res Image Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 10(7p21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.93e-06 (Chi-square test), Q value = 0.0031

Table S23.  Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 10(7P21.1) MUTATED 37 45 62 55 24
AMP PEAK 10(7P21.1) WILD-TYPE 53 49 33 45 1

Figure S23.  Get High-res Image Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 10(7p21.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.98e-08 (Chi-square test), Q value = 5.8e-05

Table S24.  Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 10(7P21.1) MUTATED 76 24 27 41 28
AMP PEAK 10(7P21.1) WILD-TYPE 22 51 27 40 16

Figure S24.  Get High-res Image Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 10(7p21.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.31e-08 (Fisher's exact test), Q value = 1.7e-05

Table S25.  Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 10(7P21.1) MUTATED 65 55 76
AMP PEAK 10(7P21.1) WILD-TYPE 87 50 19

Figure S25.  Get High-res Image Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 10(7p21.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S26.  Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 10(7P21.1) MUTATED 68 108 41
AMP PEAK 10(7P21.1) WILD-TYPE 90 75 16

Figure S26.  Get High-res Image Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 10(7p21.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000238 (Fisher's exact test), Q value = 0.13

Table S27.  Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 10(7P21.1) MUTATED 70 77 70
AMP PEAK 10(7P21.1) WILD-TYPE 93 38 50

Figure S27.  Get High-res Image Gene #10: 'Amp Peak 10(7p21.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 11(7p11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.27e-18 (Fisher's exact test), Q value = 1e-15

Table S28.  Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 11(7P11.2) MUTATED 120 66 51 15
AMP PEAK 11(7P11.2) WILD-TYPE 28 122 36 34

Figure S28.  Get High-res Image Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 11(7p11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2e-05 (Chi-square test), Q value = 0.012

Table S29.  Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 11(7P11.2) MUTATED 35 44 58 57 23
AMP PEAK 11(7P11.2) WILD-TYPE 55 50 37 43 2

Figure S29.  Get High-res Image Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 11(7p11.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000263 (Fisher's exact test), Q value = 0.14

Table S30.  Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 89 65 58
AMP PEAK 11(7P11.2) MUTATED 7 62 37 23
AMP PEAK 11(7P11.2) WILD-TYPE 16 27 28 35

Figure S30.  Get High-res Image Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 11(7p11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.09e-11 (Chi-square test), Q value = 1.6e-08

Table S31.  Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 11(7P11.2) MUTATED 77 17 28 38 27
AMP PEAK 11(7P11.2) WILD-TYPE 21 58 26 43 17

Figure S31.  Get High-res Image Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 11(7p11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-09 (Fisher's exact test), Q value = 1e-06

Table S32.  Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 11(7P11.2) MUTATED 58 54 75
AMP PEAK 11(7P11.2) WILD-TYPE 94 51 20

Figure S32.  Get High-res Image Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(7p11.2) mutation analysis' versus 'MIRSEQ_CNMF'

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

Table S33.  Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 11(7P11.2) MUTATED 59 108 41
AMP PEAK 11(7P11.2) WILD-TYPE 99 75 16

Figure S33.  Get High-res Image Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 11(7p11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.75e-07 (Fisher's exact test), Q value = 0.00033

Table S34.  Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 11(7P11.2) MUTATED 62 81 65
AMP PEAK 11(7P11.2) WILD-TYPE 101 34 55

Figure S34.  Get High-res Image Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 12(7q31.2) mutation analysis' versus 'CN_CNMF'

P value = 2.86e-09 (Fisher's exact test), Q value = 2.2e-06

Table S35.  Gene #12: 'Amp Peak 12(7q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 12(7Q31.2) MUTATED 94 54 34 18
AMP PEAK 12(7Q31.2) WILD-TYPE 54 134 53 31

Figure S35.  Get High-res Image Gene #12: 'Amp Peak 12(7q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 12(7q31.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.48e-05 (Chi-square test), Q value = 0.032

Table S36.  Gene #12: 'Amp Peak 12(7q31.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 12(7Q31.2) MUTATED 26 29 51 48 17
AMP PEAK 12(7Q31.2) WILD-TYPE 64 65 44 52 8

Figure S36.  Get High-res Image Gene #12: 'Amp Peak 12(7q31.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 12(7q31.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.03e-09 (Chi-square test), Q value = 7.9e-07

Table S37.  Gene #12: 'Amp Peak 12(7q31.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 12(7Q31.2) MUTATED 62 12 21 26 26
AMP PEAK 12(7Q31.2) WILD-TYPE 36 63 33 55 18

Figure S37.  Get High-res Image Gene #12: 'Amp Peak 12(7q31.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 12(7q31.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.03e-07 (Fisher's exact test), Q value = 7.5e-05

Table S38.  Gene #12: 'Amp Peak 12(7q31.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 12(7Q31.2) MUTATED 48 36 63
AMP PEAK 12(7Q31.2) WILD-TYPE 104 69 32

Figure S38.  Get High-res Image Gene #12: 'Amp Peak 12(7q31.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(8p11.23) mutation analysis' versus 'CN_CNMF'

P value = 2.17e-16 (Fisher's exact test), Q value = 1.7e-13

Table S39.  Gene #13: 'Amp Peak 13(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 13(8P11.23) MUTATED 34 26 28 38
AMP PEAK 13(8P11.23) WILD-TYPE 114 162 59 11

Figure S39.  Get High-res Image Gene #13: 'Amp Peak 13(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 13(8p11.23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.25e-06 (Chi-square test), Q value = 0.0051

Table S40.  Gene #13: 'Amp Peak 13(8p11.23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 13(8P11.23) MUTATED 18 45 20 19 5
AMP PEAK 13(8P11.23) WILD-TYPE 72 49 75 81 20

Figure S40.  Get High-res Image Gene #13: 'Amp Peak 13(8p11.23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 13(8p11.23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000334 (Chi-square test), Q value = 0.18

Table S41.  Gene #13: 'Amp Peak 13(8p11.23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 13(8P11.23) MUTATED 26 11 18 37 9
AMP PEAK 13(8P11.23) WILD-TYPE 72 64 36 44 35

Figure S41.  Get High-res Image Gene #13: 'Amp Peak 13(8p11.23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 13(8p11.23) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.012

Table S42.  Gene #13: 'Amp Peak 13(8p11.23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 13(8P11.23) MUTATED 29 48 24
AMP PEAK 13(8P11.23) WILD-TYPE 123 57 71

Figure S42.  Get High-res Image Gene #13: 'Amp Peak 13(8p11.23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 3.42e-21 (Fisher's exact test), Q value = 2.8e-18

Table S43.  Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 14(8P11.21) MUTATED 47 32 39 44
AMP PEAK 14(8P11.21) WILD-TYPE 101 156 48 5

Figure S43.  Get High-res Image Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 14(8p11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000128 (Chi-square test), Q value = 0.072

Table S44.  Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 14(8P11.21) MUTATED 21 51 32 29 7
AMP PEAK 14(8P11.21) WILD-TYPE 69 43 63 71 18

Figure S44.  Get High-res Image Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 14(8p11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.59e-07 (Chi-square test), Q value = 0.00032

Table S45.  Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 14(8P11.21) MUTATED 36 12 19 47 9
AMP PEAK 14(8P11.21) WILD-TYPE 62 63 35 34 35

Figure S45.  Get High-res Image Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 14(8p11.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.54e-07 (Fisher's exact test), Q value = 0.00018

Table S46.  Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 14(8P11.21) MUTATED 32 57 34
AMP PEAK 14(8P11.21) WILD-TYPE 120 48 61

Figure S46.  Get High-res Image Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(8p11.21) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.74e-05 (Fisher's exact test), Q value = 0.022

Table S47.  Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 14(8P11.21) MUTATED 36 84 19
AMP PEAK 14(8P11.21) WILD-TYPE 122 99 38

Figure S47.  Get High-res Image Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 15(8q11.1) mutation analysis' versus 'CN_CNMF'

P value = 3.04e-22 (Fisher's exact test), Q value = 2.5e-19

Table S48.  Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 15(8Q11.1) MUTATED 85 39 46 44
AMP PEAK 15(8Q11.1) WILD-TYPE 63 149 41 5

Figure S48.  Get High-res Image Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 15(8q11.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.14e-07 (Chi-square test), Q value = 8.2e-05

Table S49.  Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 15(8Q11.1) MUTATED 25 62 52 32 12
AMP PEAK 15(8Q11.1) WILD-TYPE 65 32 43 68 13

Figure S49.  Get High-res Image Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 15(8q11.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.21e-06 (Chi-square test), Q value = 0.0027

Table S50.  Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 15(8Q11.1) MUTATED 49 20 23 55 15
AMP PEAK 15(8Q11.1) WILD-TYPE 49 55 31 26 29

Figure S50.  Get High-res Image Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 15(8q11.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.93e-05 (Fisher's exact test), Q value = 0.017

Table S51.  Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 15(8Q11.1) MUTATED 50 64 48
AMP PEAK 15(8Q11.1) WILD-TYPE 102 41 47

Figure S51.  Get High-res Image Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(8q11.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.26e-07 (Fisher's exact test), Q value = 0.00023

Table S52.  Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 15(8Q11.1) MUTATED 47 108 25
AMP PEAK 15(8Q11.1) WILD-TYPE 111 75 32

Figure S52.  Get High-res Image Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 15(8q11.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.91e-06 (Fisher's exact test), Q value = 0.0031

Table S53.  Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 15(8Q11.1) MUTATED 51 57 72
AMP PEAK 15(8Q11.1) WILD-TYPE 112 58 48

Figure S53.  Get High-res Image Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 16(8q24.21) mutation analysis' versus 'CN_CNMF'

P value = 8.4e-20 (Fisher's exact test), Q value = 6.8e-17

Table S54.  Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 16(8Q24.21) MUTATED 113 73 65 47
AMP PEAK 16(8Q24.21) WILD-TYPE 35 115 22 2

Figure S54.  Get High-res Image Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 16(8q24.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.72e-08 (Chi-square test), Q value = 2.8e-05

Table S55.  Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 16(8Q24.21) MUTATED 39 76 71 50 16
AMP PEAK 16(8Q24.21) WILD-TYPE 51 18 24 50 9

Figure S55.  Get High-res Image Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 16(8q24.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.06e-07 (Chi-square test), Q value = 0.00022

Table S56.  Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 16(8Q24.21) MUTATED 74 36 26 67 22
AMP PEAK 16(8Q24.21) WILD-TYPE 24 39 28 14 22

Figure S56.  Get High-res Image Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 16(8q24.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.0082

Table S57.  Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 16(8Q24.21) MUTATED 76 77 72
AMP PEAK 16(8Q24.21) WILD-TYPE 76 28 23

Figure S57.  Get High-res Image Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 16(8q24.21) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.007

Table S58.  Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 16(8Q24.21) MUTATED 79 137 35
AMP PEAK 16(8Q24.21) WILD-TYPE 79 46 22

Figure S58.  Get High-res Image Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 16(8q24.21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.73e-05 (Fisher's exact test), Q value = 0.01

Table S59.  Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 16(8Q24.21) MUTATED 81 80 90
AMP PEAK 16(8Q24.21) WILD-TYPE 82 35 30

Figure S59.  Get High-res Image Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 17(10p15.1) mutation analysis' versus 'CN_CNMF'

P value = 4.17e-06 (Fisher's exact test), Q value = 0.0027

Table S60.  Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 17(10P15.1) MUTATED 39 29 34 22
AMP PEAK 17(10P15.1) WILD-TYPE 109 159 53 27

Figure S60.  Get High-res Image Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 17(10p15.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.59e-07 (Chi-square test), Q value = 0.00018

Table S61.  Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 17(10P15.1) MUTATED 7 39 35 20 4
AMP PEAK 17(10P15.1) WILD-TYPE 83 55 60 80 21

Figure S61.  Get High-res Image Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 17(10p15.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Chi-square test), Q value = 0.12

Table S62.  Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 17(10P15.1) MUTATED 23 11 19 35 7
AMP PEAK 17(10P15.1) WILD-TYPE 75 64 35 46 37

Figure S62.  Get High-res Image Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 17(10p15.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-06 (Fisher's exact test), Q value = 0.0015

Table S63.  Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 17(10P15.1) MUTATED 24 47 24
AMP PEAK 17(10P15.1) WILD-TYPE 128 58 71

Figure S63.  Get High-res Image Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 17(10p15.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000175 (Fisher's exact test), Q value = 0.097

Table S64.  Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 17(10P15.1) MUTATED 27 32 46
AMP PEAK 17(10P15.1) WILD-TYPE 136 83 74

Figure S64.  Get High-res Image Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 18(11q13.3) mutation analysis' versus 'CN_CNMF'

P value = 5.94e-14 (Fisher's exact test), Q value = 4.8e-11

Table S65.  Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 18(11Q13.3) MUTATED 69 24 42 22
AMP PEAK 18(11Q13.3) WILD-TYPE 79 164 45 27

Figure S65.  Get High-res Image Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 18(11q13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.94e-05 (Chi-square test), Q value = 0.012

Table S66.  Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 18(11Q13.3) MUTATED 15 43 43 25 8
AMP PEAK 18(11Q13.3) WILD-TYPE 75 51 52 75 17

Figure S66.  Get High-res Image Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 18(11q13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.18e-05 (Chi-square test), Q value = 0.019

Table S67.  Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 18(11Q13.3) MUTATED 39 12 15 43 14
AMP PEAK 18(11Q13.3) WILD-TYPE 59 63 39 38 30

Figure S67.  Get High-res Image Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 18(11q13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.55e-07 (Fisher's exact test), Q value = 0.00025

Table S68.  Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 18(11Q13.3) MUTATED 30 53 40
AMP PEAK 18(11Q13.3) WILD-TYPE 122 52 55

Figure S68.  Get High-res Image Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 18(11q13.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.77e-08 (Fisher's exact test), Q value = 3.5e-05

Table S69.  Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 18(11Q13.3) MUTATED 28 86 20
AMP PEAK 18(11Q13.3) WILD-TYPE 130 97 37

Figure S69.  Get High-res Image Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 18(11q13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.56e-08 (Fisher's exact test), Q value = 6.3e-05

Table S70.  Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 18(11Q13.3) MUTATED 30 45 59
AMP PEAK 18(11Q13.3) WILD-TYPE 133 70 61

Figure S70.  Get High-res Image Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 19(12p12.1) mutation analysis' versus 'CN_CNMF'

P value = 5.45e-22 (Fisher's exact test), Q value = 4.5e-19

Table S71.  Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 19(12P12.1) MUTATED 42 36 70 15
AMP PEAK 19(12P12.1) WILD-TYPE 106 152 17 34

Figure S71.  Get High-res Image Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 19(12p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.14e-06 (Chi-square test), Q value = 0.0027

Table S72.  Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 19(12P12.1) MUTATED 10 44 35 40 7
AMP PEAK 19(12P12.1) WILD-TYPE 80 50 60 60 18

Figure S72.  Get High-res Image Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 19(12p12.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.69e-07 (Chi-square test), Q value = 0.00065

Table S73.  Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 19(12P12.1) MUTATED 39 7 28 37 14
AMP PEAK 19(12P12.1) WILD-TYPE 59 68 26 44 30

Figure S73.  Get High-res Image Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 19(12p12.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.96e-06 (Fisher's exact test), Q value = 0.0026

Table S74.  Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 19(12P12.1) MUTATED 34 55 36
AMP PEAK 19(12P12.1) WILD-TYPE 118 50 59

Figure S74.  Get High-res Image Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 19(12p12.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0064

Table S75.  Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 19(12P12.1) MUTATED 35 85 17
AMP PEAK 19(12P12.1) WILD-TYPE 123 98 40

Figure S75.  Get High-res Image Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 19(12p12.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.46e-06 (Fisher's exact test), Q value = 0.0047

Table S76.  Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 19(12P12.1) MUTATED 34 48 55
AMP PEAK 19(12P12.1) WILD-TYPE 129 67 65

Figure S76.  Get High-res Image Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 20(12q14.1) mutation analysis' versus 'CN_CNMF'

P value = 2.65e-24 (Fisher's exact test), Q value = 2.2e-21

Table S77.  Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 20(12Q14.1) MUTATED 29 32 68 19
AMP PEAK 20(12Q14.1) WILD-TYPE 119 156 19 30

Figure S77.  Get High-res Image Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 20(12q14.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.45e-07 (Chi-square test), Q value = 1e-04

Table S78.  Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 20(12Q14.1) MUTATED 11 49 25 34 5
AMP PEAK 20(12Q14.1) WILD-TYPE 79 45 70 66 20

Figure S78.  Get High-res Image Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 20(12q14.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.68e-07 (Chi-square test), Q value = 0.00019

Table S79.  Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 20(12Q14.1) MUTATED 28 7 22 42 11
AMP PEAK 20(12Q14.1) WILD-TYPE 70 68 32 39 33

Figure S79.  Get High-res Image Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 20(12q14.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-09 (Fisher's exact test), Q value = 1.7e-06

Table S80.  Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 20(12Q14.1) MUTATED 26 57 27
AMP PEAK 20(12Q14.1) WILD-TYPE 126 48 68

Figure S80.  Get High-res Image Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(12q14.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.63e-08 (Fisher's exact test), Q value = 2e-05

Table S81.  Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 20(12Q14.1) MUTATED 26 83 14
AMP PEAK 20(12Q14.1) WILD-TYPE 132 100 43

Figure S81.  Get High-res Image Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 20(12q14.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.79e-09 (Fisher's exact test), Q value = 7.4e-06

Table S82.  Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 20(12Q14.1) MUTATED 26 38 59
AMP PEAK 20(12Q14.1) WILD-TYPE 137 77 61

Figure S82.  Get High-res Image Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.49e-21 (Fisher's exact test), Q value = 1.2e-18

Table S83.  Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 21(12Q15) MUTATED 31 34 66 20
AMP PEAK 21(12Q15) WILD-TYPE 117 154 21 29

Figure S83.  Get High-res Image Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.35e-08 (Chi-square test), Q value = 1.8e-05

Table S84.  Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 21(12Q15) MUTATED 11 52 25 32 8
AMP PEAK 21(12Q15) WILD-TYPE 79 42 70 68 17

Figure S84.  Get High-res Image Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 4.86e-07 (Chi-square test), Q value = 0.00034

Table S85.  Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 21(12Q15) MUTATED 30 8 23 42 10
AMP PEAK 21(12Q15) WILD-TYPE 68 67 31 39 34

Figure S85.  Get High-res Image Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 2.18e-07 (Fisher's exact test), Q value = 0.00015

Table S86.  Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 21(12Q15) MUTATED 32 56 25
AMP PEAK 21(12Q15) WILD-TYPE 120 49 70

Figure S86.  Get High-res Image Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.92e-07 (Fisher's exact test), Q value = 0.00014

Table S87.  Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 21(12Q15) MUTATED 29 84 15
AMP PEAK 21(12Q15) WILD-TYPE 129 99 42

Figure S87.  Get High-res Image Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 3.98e-09 (Fisher's exact test), Q value = 3e-06

Table S88.  Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 21(12Q15) MUTATED 30 34 64
AMP PEAK 21(12Q15) WILD-TYPE 133 81 56

Figure S88.  Get High-res Image Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(14q13.3) mutation analysis' versus 'CN_CNMF'

P value = 2.03e-11 (Fisher's exact test), Q value = 1.6e-08

Table S89.  Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 23(14Q13.3) MUTATED 80 48 48 35
AMP PEAK 23(14Q13.3) WILD-TYPE 68 140 39 14

Figure S89.  Get High-res Image Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 23(14q13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.73e-06 (Chi-square test), Q value = 0.003

Table S90.  Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 23(14Q13.3) MUTATED 29 56 47 31 18
AMP PEAK 23(14Q13.3) WILD-TYPE 61 38 48 69 7

Figure S90.  Get High-res Image Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 23(14q13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.55e-10 (Chi-square test), Q value = 2e-07

Table S91.  Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 23(14Q13.3) MUTATED 51 22 8 57 18
AMP PEAK 23(14Q13.3) WILD-TYPE 47 53 46 24 26

Figure S91.  Get High-res Image Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 23(14q13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.25e-05 (Fisher's exact test), Q value = 0.03

Table S92.  Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 23(14Q13.3) MUTATED 47 58 51
AMP PEAK 23(14Q13.3) WILD-TYPE 105 47 44

Figure S92.  Get High-res Image Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 23(14q13.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.37e-06 (Fisher's exact test), Q value = 0.0015

Table S93.  Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 23(14Q13.3) MUTATED 46 102 29
AMP PEAK 23(14Q13.3) WILD-TYPE 112 81 28

Figure S93.  Get High-res Image Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 23(14q13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.6e-09 (Fisher's exact test), Q value = 2.8e-06

Table S94.  Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 23(14Q13.3) MUTATED 45 55 77
AMP PEAK 23(14Q13.3) WILD-TYPE 118 60 43

Figure S94.  Get High-res Image Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 24(17q12) mutation analysis' versus 'CN_CNMF'

P value = 6.08e-14 (Fisher's exact test), Q value = 4.9e-11

Table S95.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 24(17Q12) MUTATED 90 42 52 24
AMP PEAK 24(17Q12) WILD-TYPE 58 146 35 25

Figure S95.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 24(17q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.27e-07 (Chi-square test), Q value = 0.00056

Table S96.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 24(17Q12) MUTATED 22 51 54 31 15
AMP PEAK 24(17Q12) WILD-TYPE 68 43 41 69 10

Figure S96.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 24(17q12) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.089

Table S97.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 89 65 58
AMP PEAK 24(17Q12) MUTATED 3 52 33 20
AMP PEAK 24(17Q12) WILD-TYPE 20 37 32 38

Figure S97.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 24(17q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.05e-06 (Chi-square test), Q value = 0.00071

Table S98.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 24(17Q12) MUTATED 63 21 14 42 18
AMP PEAK 24(17Q12) WILD-TYPE 35 54 40 39 26

Figure S98.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 24(17q12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.71e-08 (Fisher's exact test), Q value = 4.9e-05

Table S99.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 24(17Q12) MUTATED 44 52 62
AMP PEAK 24(17Q12) WILD-TYPE 108 53 33

Figure S99.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(17q12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.19e-06 (Fisher's exact test), Q value = 0.0021

Table S100.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 24(17Q12) MUTATED 48 105 25
AMP PEAK 24(17Q12) WILD-TYPE 110 78 32

Figure S100.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 24(17q12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.01e-07 (Fisher's exact test), Q value = 7.3e-05

Table S101.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 24(17Q12) MUTATED 47 57 74
AMP PEAK 24(17Q12) WILD-TYPE 116 58 46

Figure S101.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 25(17q23.1) mutation analysis' versus 'CN_CNMF'

P value = 2.25e-14 (Fisher's exact test), Q value = 1.8e-11

Table S102.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 25(17Q23.1) MUTATED 100 51 56 23
AMP PEAK 25(17Q23.1) WILD-TYPE 48 137 31 26

Figure S102.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 25(17q23.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.11e-08 (Chi-square test), Q value = 1.6e-05

Table S103.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 25(17Q23.1) MUTATED 24 52 65 36 15
AMP PEAK 25(17Q23.1) WILD-TYPE 66 42 30 64 10

Figure S103.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 25(17q23.1) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.12e-07 (Fisher's exact test), Q value = 0.00029

Table S104.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 89 65 58
AMP PEAK 25(17Q23.1) MUTATED 3 57 38 17
AMP PEAK 25(17Q23.1) WILD-TYPE 20 32 27 41

Figure S104.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 25(17q23.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.84e-07 (Chi-square test), Q value = 0.00013

Table S105.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 25(17Q23.1) MUTATED 70 23 17 40 19
AMP PEAK 25(17Q23.1) WILD-TYPE 28 52 37 41 25

Figure S105.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 25(17q23.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.9e-10 (Fisher's exact test), Q value = 2.3e-07

Table S106.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 25(17Q23.1) MUTATED 46 54 69
AMP PEAK 25(17Q23.1) WILD-TYPE 106 51 26

Figure S106.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(17q23.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.01

Table S107.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 25(17Q23.1) MUTATED 56 111 26
AMP PEAK 25(17Q23.1) WILD-TYPE 102 72 31

Figure S107.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 25(17q23.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.39e-06 (Fisher's exact test), Q value = 0.0034

Table S108.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 25(17Q23.1) MUTATED 55 67 71
AMP PEAK 25(17Q23.1) WILD-TYPE 108 48 49

Figure S108.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.07e-08 (Chi-square test), Q value = 8.1e-06

Table S109.  Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 26(18Q11.2) MUTATED 7 40 19 11 7
AMP PEAK 26(18Q11.2) WILD-TYPE 83 54 76 89 18

Figure S109.  Get High-res Image Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.45e-06 (Fisher's exact test), Q value = 0.00096

Table S110.  Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 26(18Q11.2) MUTATED 19 22 45
AMP PEAK 26(18Q11.2) WILD-TYPE 144 93 75

Figure S110.  Get High-res Image Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.29e-08 (Fisher's exact test), Q value = 9.7e-06

Table S111.  Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 27(19Q12) MUTATED 36 28 43 19
AMP PEAK 27(19Q12) WILD-TYPE 112 160 44 30

Figure S111.  Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000304 (Chi-square test), Q value = 0.16

Table S112.  Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 27(19Q12) MUTATED 15 41 21 25 10
AMP PEAK 27(19Q12) WILD-TYPE 75 53 74 75 15

Figure S112.  Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 4.57e-05 (Fisher's exact test), Q value = 0.026

Table S113.  Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
AMP PEAK 27(19Q12) MUTATED 24 42 30
AMP PEAK 27(19Q12) WILD-TYPE 128 63 65

Figure S113.  Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.36e-06 (Fisher's exact test), Q value = 9e-04

Table S114.  Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 27(19Q12) MUTATED 23 72 15
AMP PEAK 27(19Q12) WILD-TYPE 135 111 42

Figure S114.  Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 5.18e-07 (Fisher's exact test), Q value = 0.00036

Table S115.  Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 27(19Q12) MUTATED 23 37 50
AMP PEAK 27(19Q12) WILD-TYPE 140 78 70

Figure S115.  Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(20p11.21) mutation analysis' versus 'CN_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0067

Table S116.  Gene #28: 'Amp Peak 28(20p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 28(20P11.21) MUTATED 53 52 44 30
AMP PEAK 28(20P11.21) WILD-TYPE 95 136 43 19

Figure S116.  Get High-res Image Gene #28: 'Amp Peak 28(20p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 28(20p11.21) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.13

Table S117.  Gene #28: 'Amp Peak 28(20p11.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 28(20P11.21) MUTATED 43 89 21
AMP PEAK 28(20P11.21) WILD-TYPE 115 94 36

Figure S117.  Get High-res Image Gene #28: 'Amp Peak 28(20p11.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 28(20p11.21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.44e-05 (Fisher's exact test), Q value = 0.02

Table S118.  Gene #28: 'Amp Peak 28(20p11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 28(20P11.21) MUTATED 43 47 63
AMP PEAK 28(20P11.21) WILD-TYPE 120 68 57

Figure S118.  Get High-res Image Gene #28: 'Amp Peak 28(20p11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 29(20q13.33) mutation analysis' versus 'CN_CNMF'

P value = 1.03e-07 (Fisher's exact test), Q value = 7.5e-05

Table S119.  Gene #29: 'Amp Peak 29(20q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 29(20Q13.33) MUTATED 77 61 52 35
AMP PEAK 29(20Q13.33) WILD-TYPE 71 127 35 14

Figure S119.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 29(20q13.33) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.15e-05 (Chi-square test), Q value = 0.007

Table S120.  Gene #29: 'Amp Peak 29(20q13.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 29(20Q13.33) MUTATED 50 26 18 58 22
AMP PEAK 29(20Q13.33) WILD-TYPE 48 49 36 23 22

Figure S120.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 29(20q13.33) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.0063

Table S121.  Gene #29: 'Amp Peak 29(20q13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
AMP PEAK 29(20Q13.33) MUTATED 54 110 27
AMP PEAK 29(20Q13.33) WILD-TYPE 104 73 30

Figure S121.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 29(20q13.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.34e-05 (Fisher's exact test), Q value = 0.0081

Table S122.  Gene #29: 'Amp Peak 29(20q13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
AMP PEAK 29(20Q13.33) MUTATED 56 61 74
AMP PEAK 29(20Q13.33) WILD-TYPE 107 54 46

Figure S122.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 31(Xq28) mutation analysis' versus 'CN_CNMF'

P value = 3.01e-10 (Fisher's exact test), Q value = 2.3e-07

Table S123.  Gene #31: 'Amp Peak 31(Xq28) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
AMP PEAK 31(XQ28) MUTATED 73 29 31 18
AMP PEAK 31(XQ28) WILD-TYPE 75 159 56 31

Figure S123.  Get High-res Image Gene #31: 'Amp Peak 31(Xq28) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 31(Xq28) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.94e-05 (Chi-square test), Q value = 0.034

Table S124.  Gene #31: 'Amp Peak 31(Xq28) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
AMP PEAK 31(XQ28) MUTATED 15 34 43 22 11
AMP PEAK 31(XQ28) WILD-TYPE 75 60 52 78 14

Figure S124.  Get High-res Image Gene #31: 'Amp Peak 31(Xq28) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 31(Xq28) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000272 (Chi-square test), Q value = 0.15

Table S125.  Gene #31: 'Amp Peak 31(Xq28) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
AMP PEAK 31(XQ28) MUTATED 49 15 12 29 14
AMP PEAK 31(XQ28) WILD-TYPE 49 60 42 52 30

Figure S125.  Get High-res Image Gene #31: 'Amp Peak 31(Xq28) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 1.59e-06 (Fisher's exact test), Q value = 0.0011

Table S126.  Gene #32: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 1(1P36.13) MUTATED 19 38 27 24
DEL PEAK 1(1P36.13) WILD-TYPE 129 150 60 25

Figure S126.  Get High-res Image Gene #32: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.18e-05 (Chi-square test), Q value = 0.013

Table S127.  Gene #32: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 1(1P36.13) MUTATED 11 38 22 15 4
DEL PEAK 1(1P36.13) WILD-TYPE 79 56 73 85 21

Figure S127.  Get High-res Image Gene #32: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 5.33e-05 (Chi-square test), Q value = 0.031

Table S128.  Gene #32: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 1(1P36.13) MUTATED 19 13 20 28 1
DEL PEAK 1(1P36.13) WILD-TYPE 79 62 34 53 43

Figure S128.  Get High-res Image Gene #32: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 0.000179 (Fisher's exact test), Q value = 0.099

Table S129.  Gene #32: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 1(1P36.13) MUTATED 21 38 22
DEL PEAK 1(1P36.13) WILD-TYPE 131 67 73

Figure S129.  Get High-res Image Gene #32: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000215 (Fisher's exact test), Q value = 0.12

Table S130.  Gene #32: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 1(1P36.13) MUTATED 27 57 5
DEL PEAK 1(1P36.13) WILD-TYPE 131 126 52

Figure S130.  Get High-res Image Gene #32: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 9.97e-07 (Fisher's exact test), Q value = 0.00067

Table S131.  Gene #33: 'Del Peak 2(1p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 2(1P13.3) MUTATED 29 46 37 27
DEL PEAK 2(1P13.3) WILD-TYPE 119 142 50 22

Figure S131.  Get High-res Image Gene #33: 'Del Peak 2(1p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 9.81e-05 (Chi-square test), Q value = 0.056

Table S132.  Gene #33: 'Del Peak 2(1p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 2(1P13.3) MUTATED 25 41 27 13 5
DEL PEAK 2(1P13.3) WILD-TYPE 65 53 68 87 20

Figure S132.  Get High-res Image Gene #33: 'Del Peak 2(1p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.93e-06 (Fisher's exact test), Q value = 0.0013

Table S133.  Gene #34: 'Del Peak 3(1p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 3(1P13.1) MUTATED 31 42 40 24
DEL PEAK 3(1P13.1) WILD-TYPE 117 146 47 25

Figure S133.  Get High-res Image Gene #34: 'Del Peak 3(1p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.2e-05 (Chi-square test), Q value = 0.013

Table S134.  Gene #34: 'Del Peak 3(1p13.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 3(1P13.1) MUTATED 22 40 32 12 4
DEL PEAK 3(1P13.1) WILD-TYPE 68 54 63 88 21

Figure S134.  Get High-res Image Gene #34: 'Del Peak 3(1p13.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 5(2q37.3) mutation analysis' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.18

Table S135.  Gene #36: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 5(2Q37.3) MUTATED 30 12 10 11
DEL PEAK 5(2Q37.3) WILD-TYPE 118 176 77 38

Figure S135.  Get High-res Image Gene #36: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 6(3p21.31) mutation analysis' versus 'CN_CNMF'

P value = 7.53e-06 (Fisher's exact test), Q value = 0.0047

Table S136.  Gene #37: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 6(3P21.31) MUTATED 77 65 53 32
DEL PEAK 6(3P21.31) WILD-TYPE 71 123 34 17

Figure S136.  Get High-res Image Gene #37: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 6(3p21.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.21e-06 (Chi-square test), Q value = 0.0021

Table S137.  Gene #37: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 6(3P21.31) MUTATED 32 67 43 39 15
DEL PEAK 6(3P21.31) WILD-TYPE 58 27 52 61 10

Figure S137.  Get High-res Image Gene #37: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 6(3p21.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.35e-09 (Fisher's exact test), Q value = 2.6e-06

Table S138.  Gene #37: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 6(3P21.31) MUTATED 49 75 47
DEL PEAK 6(3P21.31) WILD-TYPE 103 30 48

Figure S138.  Get High-res Image Gene #37: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(3p21.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.43e-06 (Fisher's exact test), Q value = 0.0052

Table S139.  Gene #37: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 6(3P21.31) MUTATED 52 106 32
DEL PEAK 6(3P21.31) WILD-TYPE 106 77 25

Figure S139.  Get High-res Image Gene #37: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 6(3p21.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-06 (Fisher's exact test), Q value = 0.0019

Table S140.  Gene #37: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 6(3P21.31) MUTATED 55 59 76
DEL PEAK 6(3P21.31) WILD-TYPE 108 56 44

Figure S140.  Get High-res Image Gene #37: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(3q29) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.11e-05 (Chi-square test), Q value = 0.046

Table S141.  Gene #39: 'Del Peak 8(3q29) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 8(3Q29) MUTATED 35 36 29 11 7
DEL PEAK 8(3Q29) WILD-TYPE 55 58 66 89 18

Figure S141.  Get High-res Image Gene #39: 'Del Peak 8(3q29) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 8(3q29) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.83e-05 (Chi-square test), Q value = 0.05

Table S142.  Gene #39: 'Del Peak 8(3q29) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 8(3Q29) MUTATED 16 26 10 37 10
DEL PEAK 8(3Q29) WILD-TYPE 82 49 44 44 34

Figure S142.  Get High-res Image Gene #39: 'Del Peak 8(3q29) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0094

Table S143.  Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 9(4P16.3) MUTATED 37 28 28 23
DEL PEAK 9(4P16.3) WILD-TYPE 111 160 59 26

Figure S143.  Get High-res Image Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.31e-05 (Chi-square test), Q value = 0.014

Table S144.  Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 9(4P16.3) MUTATED 7 38 22 26 7
DEL PEAK 9(4P16.3) WILD-TYPE 83 56 73 74 18

Figure S144.  Get High-res Image Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 9.45e-07 (Chi-square test), Q value = 0.00064

Table S145.  Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 9(4P16.3) MUTATED 21 6 16 37 7
DEL PEAK 9(4P16.3) WILD-TYPE 77 69 38 44 37

Figure S145.  Get High-res Image Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3.34e-07 (Fisher's exact test), Q value = 0.00023

Table S146.  Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 9(4P16.3) MUTATED 21 46 20
DEL PEAK 9(4P16.3) WILD-TYPE 131 59 75

Figure S146.  Get High-res Image Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 6.15e-07 (Fisher's exact test), Q value = 0.00042

Table S147.  Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 9(4P16.3) MUTATED 19 67 14
DEL PEAK 9(4P16.3) WILD-TYPE 139 116 43

Figure S147.  Get High-res Image Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 4.73e-08 (Fisher's exact test), Q value = 3.5e-05

Table S148.  Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 9(4P16.3) MUTATED 20 29 51
DEL PEAK 9(4P16.3) WILD-TYPE 143 86 69

Figure S148.  Get High-res Image Gene #40: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(4q22.1) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.12

Table S149.  Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
DEL PEAK 10(4Q22.1) MUTATED 3 1 0 5
DEL PEAK 10(4Q22.1) WILD-TYPE 2 8 12 1

Figure S149.  Get High-res Image Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 10(4q22.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.89e-05 (Fisher's exact test), Q value = 0.056

Table S150.  Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 13 12
DEL PEAK 10(4Q22.1) MUTATED 6 0 3
DEL PEAK 10(4Q22.1) WILD-TYPE 1 13 9

Figure S150.  Get High-res Image Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 10(4q22.1) mutation analysis' versus 'CN_CNMF'

P value = 3.67e-07 (Fisher's exact test), Q value = 0.00026

Table S151.  Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 10(4Q22.1) MUTATED 48 32 42 20
DEL PEAK 10(4Q22.1) WILD-TYPE 100 156 45 29

Figure S151.  Get High-res Image Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 10(4q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.89e-08 (Chi-square test), Q value = 7.2e-05

Table S152.  Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 10(4Q22.1) MUTATED 8 45 25 29 12
DEL PEAK 10(4Q22.1) WILD-TYPE 82 49 70 71 13

Figure S152.  Get High-res Image Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 10(4q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.41e-07 (Chi-square test), Q value = 0.00037

Table S153.  Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 10(4Q22.1) MUTATED 24 9 24 40 9
DEL PEAK 10(4Q22.1) WILD-TYPE 74 66 30 41 35

Figure S153.  Get High-res Image Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 10(4q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.52e-12 (Fisher's exact test), Q value = 2.8e-09

Table S154.  Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 10(4Q22.1) MUTATED 23 60 23
DEL PEAK 10(4Q22.1) WILD-TYPE 129 45 72

Figure S154.  Get High-res Image Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(4q22.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.18e-07 (Fisher's exact test), Q value = 0.00036

Table S155.  Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 10(4Q22.1) MUTATED 25 77 16
DEL PEAK 10(4Q22.1) WILD-TYPE 133 106 41

Figure S155.  Get High-res Image Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 10(4q22.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.14e-08 (Fisher's exact test), Q value = 8.6e-06

Table S156.  Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 10(4Q22.1) MUTATED 25 35 58
DEL PEAK 10(4Q22.1) WILD-TYPE 138 80 62

Figure S156.  Get High-res Image Gene #41: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(4q35.1) mutation analysis' versus 'CN_CNMF'

P value = 7.48e-10 (Fisher's exact test), Q value = 5.8e-07

Table S157.  Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 11(4Q35.1) MUTATED 58 38 50 26
DEL PEAK 11(4Q35.1) WILD-TYPE 90 150 37 23

Figure S157.  Get High-res Image Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 11(4q35.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.36e-11 (Chi-square test), Q value = 1.1e-08

Table S158.  Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 11(4Q35.1) MUTATED 8 58 35 35 12
DEL PEAK 11(4Q35.1) WILD-TYPE 82 36 60 65 13

Figure S158.  Get High-res Image Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 11(4q35.1) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000196 (Fisher's exact test), Q value = 0.11

Table S159.  Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 89 65 58
DEL PEAK 11(4Q35.1) MUTATED 11 32 39 13
DEL PEAK 11(4Q35.1) WILD-TYPE 12 57 26 45

Figure S159.  Get High-res Image Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 11(4q35.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.07e-11 (Chi-square test), Q value = 1.6e-08

Table S160.  Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 11(4Q35.1) MUTATED 27 10 26 53 11
DEL PEAK 11(4Q35.1) WILD-TYPE 71 65 28 28 33

Figure S160.  Get High-res Image Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 11(4q35.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.71e-17 (Fisher's exact test), Q value = 6.2e-14

Table S161.  Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 11(4Q35.1) MUTATED 28 73 26
DEL PEAK 11(4Q35.1) WILD-TYPE 124 32 69

Figure S161.  Get High-res Image Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(4q35.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.07e-08 (Fisher's exact test), Q value = 8.1e-06

Table S162.  Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 11(4Q35.1) MUTATED 34 94 14
DEL PEAK 11(4Q35.1) WILD-TYPE 124 89 43

Figure S162.  Get High-res Image Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 11(4q35.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.67e-14 (Fisher's exact test), Q value = 1.3e-11

Table S163.  Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 11(4Q35.1) MUTATED 31 34 77
DEL PEAK 11(4Q35.1) WILD-TYPE 132 81 43

Figure S163.  Get High-res Image Gene #42: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.9e-12 (Fisher's exact test), Q value = 1.5e-09

Table S164.  Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 12(5Q11.2) MUTATED 70 29 44 23
DEL PEAK 12(5Q11.2) WILD-TYPE 78 159 43 26

Figure S164.  Get High-res Image Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(5q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.02e-07 (Chi-square test), Q value = 0.00014

Table S165.  Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 12(5Q11.2) MUTATED 12 47 35 29 15
DEL PEAK 12(5Q11.2) WILD-TYPE 78 47 60 71 10

Figure S165.  Get High-res Image Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 12(5q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.01e-05 (Chi-square test), Q value = 0.0062

Table S166.  Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 12(5Q11.2) MUTATED 41 11 16 43 13
DEL PEAK 12(5Q11.2) WILD-TYPE 57 64 38 38 31

Figure S166.  Get High-res Image Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 12(5q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.77e-08 (Fisher's exact test), Q value = 5.7e-05

Table S167.  Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 12(5Q11.2) MUTATED 30 56 38
DEL PEAK 12(5Q11.2) WILD-TYPE 122 49 57

Figure S167.  Get High-res Image Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(5q11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.54e-07 (Fisher's exact test), Q value = 0.00032

Table S168.  Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 12(5Q11.2) MUTATED 34 90 18
DEL PEAK 12(5Q11.2) WILD-TYPE 124 93 39

Figure S168.  Get High-res Image Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 12(5q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.44e-08 (Fisher's exact test), Q value = 5.5e-05

Table S169.  Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 12(5Q11.2) MUTATED 34 44 64
DEL PEAK 12(5Q11.2) WILD-TYPE 129 71 56

Figure S169.  Get High-res Image Gene #43: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(5q22.1) mutation analysis' versus 'CN_CNMF'

P value = 1.08e-12 (Fisher's exact test), Q value = 8.6e-10

Table S170.  Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 13(5Q22.1) MUTATED 75 37 52 25
DEL PEAK 13(5Q22.1) WILD-TYPE 73 151 35 24

Figure S170.  Get High-res Image Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(5q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.56e-08 (Chi-square test), Q value = 1.9e-05

Table S171.  Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 13(5Q22.1) MUTATED 14 52 43 37 17
DEL PEAK 13(5Q22.1) WILD-TYPE 76 42 52 63 8

Figure S171.  Get High-res Image Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 13(5q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.18e-07 (Chi-square test), Q value = 0.00042

Table S172.  Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 13(5Q22.1) MUTATED 48 13 18 49 16
DEL PEAK 13(5Q22.1) WILD-TYPE 50 62 36 32 28

Figure S172.  Get High-res Image Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 13(5q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.49e-08 (Fisher's exact test), Q value = 1.9e-05

Table S173.  Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 13(5Q22.1) MUTATED 37 63 44
DEL PEAK 13(5Q22.1) WILD-TYPE 115 42 51

Figure S173.  Get High-res Image Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(5q22.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.2e-09 (Fisher's exact test), Q value = 9.2e-07

Table S174.  Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 13(5Q22.1) MUTATED 39 106 19
DEL PEAK 13(5Q22.1) WILD-TYPE 119 77 38

Figure S174.  Get High-res Image Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 13(5q22.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.45e-09 (Fisher's exact test), Q value = 1.1e-06

Table S175.  Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 13(5Q22.1) MUTATED 38 55 71
DEL PEAK 13(5Q22.1) WILD-TYPE 125 60 49

Figure S175.  Get High-res Image Gene #44: 'Del Peak 13(5q22.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(6q22.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.29e-06 (Chi-square test), Q value = 0.00086

Table S176.  Gene #46: 'Del Peak 15(6q22.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 15(6Q22.31) MUTATED 51 52 62 28 9
DEL PEAK 15(6Q22.31) WILD-TYPE 39 42 33 72 16

Figure S176.  Get High-res Image Gene #46: 'Del Peak 15(6q22.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 16(6q26) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.64e-05 (Chi-square test), Q value = 0.049

Table S177.  Gene #47: 'Del Peak 16(6q26) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 16(6Q26) MUTATED 49 54 58 31 9
DEL PEAK 16(6Q26) WILD-TYPE 41 40 37 69 16

Figure S177.  Get High-res Image Gene #47: 'Del Peak 16(6q26) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 17(8p23.2) mutation analysis' versus 'CN_CNMF'

P value = 7.67e-17 (Fisher's exact test), Q value = 6.2e-14

Table S178.  Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 17(8P23.2) MUTATED 107 49 51 22
DEL PEAK 17(8P23.2) WILD-TYPE 41 139 36 27

Figure S178.  Get High-res Image Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 17(8p23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.17e-05 (Chi-square test), Q value = 0.052

Table S179.  Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 17(8P23.2) MUTATED 26 45 58 47 17
DEL PEAK 17(8P23.2) WILD-TYPE 64 49 37 53 8

Figure S179.  Get High-res Image Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 17(8p23.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000354 (Fisher's exact test), Q value = 0.19

Table S180.  Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 89 65 58
DEL PEAK 17(8P23.2) MUTATED 10 56 34 16
DEL PEAK 17(8P23.2) WILD-TYPE 13 33 31 42

Figure S180.  Get High-res Image Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 17(8p23.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.05e-05 (Chi-square test), Q value = 0.0064

Table S181.  Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 17(8P23.2) MUTATED 67 23 20 43 22
DEL PEAK 17(8P23.2) WILD-TYPE 31 52 34 38 22

Figure S181.  Get High-res Image Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 17(8p23.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.83e-07 (Fisher's exact test), Q value = 0.00013

Table S182.  Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 17(8P23.2) MUTATED 54 53 68
DEL PEAK 17(8P23.2) WILD-TYPE 98 52 27

Figure S182.  Get High-res Image Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(8p23.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.67e-06 (Fisher's exact test), Q value = 0.0011

Table S183.  Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 17(8P23.2) MUTATED 57 76 61
DEL PEAK 17(8P23.2) WILD-TYPE 106 39 59

Figure S183.  Get High-res Image Gene #48: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(8p12) mutation analysis' versus 'CN_CNMF'

P value = 1.83e-15 (Fisher's exact test), Q value = 1.5e-12

Table S184.  Gene #49: 'Del Peak 18(8p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 18(8P12) MUTATED 101 45 43 16
DEL PEAK 18(8P12) WILD-TYPE 47 143 44 33

Figure S184.  Get High-res Image Gene #49: 'Del Peak 18(8p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 18(8p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.95e-05 (Chi-square test), Q value = 0.012

Table S185.  Gene #49: 'Del Peak 18(8p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 18(8P12) MUTATED 23 39 54 43 18
DEL PEAK 18(8P12) WILD-TYPE 67 55 41 57 7

Figure S185.  Get High-res Image Gene #49: 'Del Peak 18(8p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 18(8p12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000262 (Chi-square test), Q value = 0.14

Table S186.  Gene #49: 'Del Peak 18(8p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 18(8P12) MUTATED 61 22 21 35 16
DEL PEAK 18(8P12) WILD-TYPE 37 53 33 46 28

Figure S186.  Get High-res Image Gene #49: 'Del Peak 18(8p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 18(8p12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.86e-06 (Fisher's exact test), Q value = 0.0049

Table S187.  Gene #49: 'Del Peak 18(8p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 18(8P12) MUTATED 50 44 61
DEL PEAK 18(8P12) WILD-TYPE 102 61 34

Figure S187.  Get High-res Image Gene #49: 'Del Peak 18(8p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(8p12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.8e-06 (Fisher's exact test), Q value = 0.0049

Table S188.  Gene #49: 'Del Peak 18(8p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 18(8P12) MUTATED 49 67 58
DEL PEAK 18(8P12) WILD-TYPE 114 48 62

Figure S188.  Get High-res Image Gene #49: 'Del Peak 18(8p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 2.79e-11 (Fisher's exact test), Q value = 2.2e-08

Table S189.  Gene #50: 'Del Peak 19(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 19(8P11.21) MUTATED 59 27 21 0
DEL PEAK 19(8P11.21) WILD-TYPE 89 161 66 49

Figure S189.  Get High-res Image Gene #50: 'Del Peak 19(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 21(9p23) mutation analysis' versus 'CN_CNMF'

P value = 3.22e-07 (Fisher's exact test), Q value = 0.00023

Table S190.  Gene #52: 'Del Peak 21(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 21(9P23) MUTATED 88 85 67 18
DEL PEAK 21(9P23) WILD-TYPE 60 103 20 31

Figure S190.  Get High-res Image Gene #52: 'Del Peak 21(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 22(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.0012

Table S191.  Gene #53: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 22(9P21.3) MUTATED 91 89 66 18
DEL PEAK 22(9P21.3) WILD-TYPE 57 99 21 31

Figure S191.  Get High-res Image Gene #53: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 23(9q21.11) mutation analysis' versus 'CN_CNMF'

P value = 1.49e-07 (Fisher's exact test), Q value = 0.00011

Table S192.  Gene #54: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 23(9Q21.11) MUTATED 73 66 61 31
DEL PEAK 23(9Q21.11) WILD-TYPE 75 122 26 18

Figure S192.  Get High-res Image Gene #54: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 23(9q21.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.08e-05 (Chi-square test), Q value = 0.029

Table S193.  Gene #54: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 23(9Q21.11) MUTATED 36 66 36 46 13
DEL PEAK 23(9Q21.11) WILD-TYPE 54 28 59 54 12

Figure S193.  Get High-res Image Gene #54: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 23(9q21.11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.41e-06 (Fisher's exact test), Q value = 0.0058

Table S194.  Gene #54: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 23(9Q21.11) MUTATED 59 72 43
DEL PEAK 23(9Q21.11) WILD-TYPE 93 33 52

Figure S194.  Get High-res Image Gene #54: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 23(9q21.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.0073

Table S195.  Gene #54: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 23(9Q21.11) MUTATED 60 61 78
DEL PEAK 23(9Q21.11) WILD-TYPE 103 54 42

Figure S195.  Get High-res Image Gene #54: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(10q26.3) mutation analysis' versus 'CN_CNMF'

P value = 4.78e-06 (Fisher's exact test), Q value = 0.0031

Table S196.  Gene #56: 'Del Peak 25(10q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 25(10Q26.3) MUTATED 63 32 21 14
DEL PEAK 25(10Q26.3) WILD-TYPE 85 156 66 35

Figure S196.  Get High-res Image Gene #56: 'Del Peak 25(10q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 25(10q26.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000256 (Chi-square test), Q value = 0.14

Table S197.  Gene #56: 'Del Peak 25(10q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 25(10Q26.3) MUTATED 18 31 29 16 14
DEL PEAK 25(10Q26.3) WILD-TYPE 72 63 66 84 11

Figure S197.  Get High-res Image Gene #56: 'Del Peak 25(10q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 4.04e-06 (Fisher's exact test), Q value = 0.0026

Table S198.  Gene #57: 'Del Peak 26(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 26(11P15.5) MUTATED 54 27 32 13
DEL PEAK 26(11P15.5) WILD-TYPE 94 161 55 36

Figure S198.  Get High-res Image Gene #57: 'Del Peak 26(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 5.3e-06 (Fisher's exact test), Q value = 0.0034

Table S199.  Gene #57: 'Del Peak 26(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 26(11P15.5) MUTATED 22 44 26
DEL PEAK 26(11P15.5) WILD-TYPE 130 61 69

Figure S199.  Get High-res Image Gene #57: 'Del Peak 26(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000122 (Fisher's exact test), Q value = 0.069

Table S200.  Gene #58: 'Del Peak 27(11q23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 27(11Q23.2) MUTATED 30 29 32 18
DEL PEAK 27(11Q23.2) WILD-TYPE 118 159 55 31

Figure S200.  Get High-res Image Gene #58: 'Del Peak 27(11q23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 28(11q25) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000464 (Chi-square test), Q value = 0.25

Table S201.  Gene #59: 'Del Peak 28(11q25) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 28(11Q25) MUTATED 15 11 21 26 6
DEL PEAK 28(11Q25) WILD-TYPE 83 64 33 55 38

Figure S201.  Get High-res Image Gene #59: 'Del Peak 28(11q25) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 29(12p13.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000172 (Fisher's exact test), Q value = 0.095

Table S202.  Gene #60: 'Del Peak 29(12p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 29(12P13.2) MUTATED 59 41 14 12
DEL PEAK 29(12P13.2) WILD-TYPE 89 147 73 37

Figure S202.  Get High-res Image Gene #60: 'Del Peak 29(12p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 29(12p13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.21e-07 (Chi-square test), Q value = 0.00049

Table S203.  Gene #60: 'Del Peak 29(12p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 29(12P13.2) MUTATED 24 17 34 14 16
DEL PEAK 29(12P13.2) WILD-TYPE 66 77 61 86 9

Figure S203.  Get High-res Image Gene #60: 'Del Peak 29(12p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 30(12q12) mutation analysis' versus 'CN_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0072

Table S204.  Gene #61: 'Del Peak 30(12q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 30(12Q12) MUTATED 47 29 6 8
DEL PEAK 30(12Q12) WILD-TYPE 101 159 81 41

Figure S204.  Get High-res Image Gene #61: 'Del Peak 30(12q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 31(12q24.33) mutation analysis' versus 'CN_CNMF'

P value = 6.54e-06 (Fisher's exact test), Q value = 0.0041

Table S205.  Gene #62: 'Del Peak 31(12q24.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 31(12Q24.33) MUTATED 55 45 10 5
DEL PEAK 31(12Q24.33) WILD-TYPE 93 143 77 44

Figure S205.  Get High-res Image Gene #62: 'Del Peak 31(12q24.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 31(12q24.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.84e-06 (Fisher's exact test), Q value = 0.0037

Table S206.  Gene #62: 'Del Peak 31(12q24.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 31(12Q24.33) MUTATED 54 28 11
DEL PEAK 31(12Q24.33) WILD-TYPE 109 87 109

Figure S206.  Get High-res Image Gene #62: 'Del Peak 31(12q24.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(13q12.11) mutation analysis' versus 'CN_CNMF'

P value = 1.38e-19 (Fisher's exact test), Q value = 1.1e-16

Table S207.  Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 32(13Q12.11) MUTATED 118 58 59 30
DEL PEAK 32(13Q12.11) WILD-TYPE 30 130 28 19

Figure S207.  Get High-res Image Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 32(13q12.11) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.00098

Table S208.  Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 89 65 58
DEL PEAK 32(13Q12.11) MUTATED 8 66 39 19
DEL PEAK 32(13Q12.11) WILD-TYPE 15 23 26 39

Figure S208.  Get High-res Image Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 32(13q12.11) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.36e-06 (Chi-square test), Q value = 0.0015

Table S209.  Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 32(13Q12.11) MUTATED 66 27 25 59 19
DEL PEAK 32(13Q12.11) WILD-TYPE 32 48 29 22 25

Figure S209.  Get High-res Image Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 32(13q12.11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.99e-09 (Fisher's exact test), Q value = 3e-06

Table S210.  Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 32(13Q12.11) MUTATED 56 74 66
DEL PEAK 32(13Q12.11) WILD-TYPE 96 31 29

Figure S210.  Get High-res Image Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(13q12.11) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.35e-06 (Fisher's exact test), Q value = 0.0046

Table S211.  Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 32(13Q12.11) MUTATED 66 124 34
DEL PEAK 32(13Q12.11) WILD-TYPE 92 59 23

Figure S211.  Get High-res Image Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 32(13q12.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.66e-07 (Fisher's exact test), Q value = 0.00059

Table S212.  Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 32(13Q12.11) MUTATED 66 77 81
DEL PEAK 32(13Q12.11) WILD-TYPE 97 38 39

Figure S212.  Get High-res Image Gene #63: 'Del Peak 32(13q12.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(13q12.13) mutation analysis' versus 'CN_CNMF'

P value = 1.05e-19 (Fisher's exact test), Q value = 8.5e-17

Table S213.  Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 33(13Q12.13) MUTATED 120 59 56 31
DEL PEAK 33(13Q12.13) WILD-TYPE 28 129 31 18

Figure S213.  Get High-res Image Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 33(13q12.13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000107 (Chi-square test), Q value = 0.061

Table S214.  Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 33(13Q12.13) MUTATED 38 59 66 49 20
DEL PEAK 33(13Q12.13) WILD-TYPE 52 35 29 51 5

Figure S214.  Get High-res Image Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 33(13q12.13) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 6.68e-07 (Fisher's exact test), Q value = 0.00046

Table S215.  Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 89 65 58
DEL PEAK 33(13Q12.13) MUTATED 8 67 39 19
DEL PEAK 33(13Q12.13) WILD-TYPE 15 22 26 39

Figure S215.  Get High-res Image Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 33(13q12.13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.8e-06 (Chi-square test), Q value = 0.0031

Table S216.  Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 33(13Q12.13) MUTATED 66 28 25 59 19
DEL PEAK 33(13Q12.13) WILD-TYPE 32 47 29 22 25

Figure S216.  Get High-res Image Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 33(13q12.13) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.61e-09 (Fisher's exact test), Q value = 6.5e-06

Table S217.  Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 33(13Q12.13) MUTATED 57 73 67
DEL PEAK 33(13Q12.13) WILD-TYPE 95 32 28

Figure S217.  Get High-res Image Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(13q12.13) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.21e-05 (Fisher's exact test), Q value = 0.019

Table S218.  Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 33(13Q12.13) MUTATED 67 122 34
DEL PEAK 33(13Q12.13) WILD-TYPE 91 61 23

Figure S218.  Get High-res Image Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 33(13q12.13) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.52e-06 (Fisher's exact test), Q value = 0.0023

Table S219.  Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 33(13Q12.13) MUTATED 67 75 81
DEL PEAK 33(13Q12.13) WILD-TYPE 96 40 39

Figure S219.  Get High-res Image Gene #64: 'Del Peak 33(13q12.13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(13q14.2) mutation analysis' versus 'CN_CNMF'

P value = 7.61e-22 (Fisher's exact test), Q value = 6.2e-19

Table S220.  Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 34(13Q14.2) MUTATED 117 52 52 35
DEL PEAK 34(13Q14.2) WILD-TYPE 31 136 35 14

Figure S220.  Get High-res Image Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 34(13q14.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0064

Table S221.  Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 89 65 58
DEL PEAK 34(13Q14.2) MUTATED 8 60 40 17
DEL PEAK 34(13Q14.2) WILD-TYPE 15 29 25 41

Figure S221.  Get High-res Image Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 34(13q14.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.81e-07 (Chi-square test), Q value = 0.00059

Table S222.  Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 34(13Q14.2) MUTATED 64 23 22 56 20
DEL PEAK 34(13Q14.2) WILD-TYPE 34 52 32 25 24

Figure S222.  Get High-res Image Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 34(13q14.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.07e-08 (Fisher's exact test), Q value = 3e-05

Table S223.  Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 34(13Q14.2) MUTATED 53 68 64
DEL PEAK 34(13Q14.2) WILD-TYPE 99 37 31

Figure S223.  Get High-res Image Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(13q14.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.019

Table S224.  Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 34(13Q14.2) MUTATED 62 116 33
DEL PEAK 34(13Q14.2) WILD-TYPE 96 67 24

Figure S224.  Get High-res Image Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 34(13q14.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.26e-06 (Fisher's exact test), Q value = 0.00084

Table S225.  Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 34(13Q14.2) MUTATED 61 72 78
DEL PEAK 34(13Q14.2) WILD-TYPE 102 43 42

Figure S225.  Get High-res Image Gene #65: 'Del Peak 34(13q14.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 35(13q34) mutation analysis' versus 'CN_CNMF'

P value = 2.2e-15 (Fisher's exact test), Q value = 1.8e-12

Table S226.  Gene #66: 'Del Peak 35(13q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 35(13Q34) MUTATED 95 43 49 30
DEL PEAK 35(13Q34) WILD-TYPE 53 145 38 19

Figure S226.  Get High-res Image Gene #66: 'Del Peak 35(13q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 35(13q34) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.88e-05 (Chi-square test), Q value = 0.023

Table S227.  Gene #66: 'Del Peak 35(13q34) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 35(13Q34) MUTATED 52 21 18 51 17
DEL PEAK 35(13Q34) WILD-TYPE 46 54 36 30 27

Figure S227.  Get High-res Image Gene #66: 'Del Peak 35(13q34) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 35(13q34) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.1e-06 (Fisher's exact test), Q value = 0.0032

Table S228.  Gene #66: 'Del Peak 35(13q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 35(13Q34) MUTATED 46 59 54
DEL PEAK 35(13Q34) WILD-TYPE 106 46 41

Figure S228.  Get High-res Image Gene #66: 'Del Peak 35(13q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(13q34) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.13

Table S229.  Gene #66: 'Del Peak 35(13q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 35(13Q34) MUTATED 54 63 63
DEL PEAK 35(13Q34) WILD-TYPE 109 52 57

Figure S229.  Get High-res Image Gene #66: 'Del Peak 35(13q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 36(14q32.33) mutation analysis' versus 'CN_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.076

Table S230.  Gene #67: 'Del Peak 36(14q32.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 36(14Q32.33) MUTATED 46 46 41 7
DEL PEAK 36(14Q32.33) WILD-TYPE 102 142 46 42

Figure S230.  Get High-res Image Gene #67: 'Del Peak 36(14q32.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 37(15q11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.81e-10 (Fisher's exact test), Q value = 1.4e-07

Table S231.  Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 37(15Q11.2) MUTATED 104 63 42 30
DEL PEAK 37(15Q11.2) WILD-TYPE 44 125 45 19

Figure S231.  Get High-res Image Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 37(15q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000193 (Chi-square test), Q value = 0.11

Table S232.  Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 37(15Q11.2) MUTATED 31 48 59 45 19
DEL PEAK 37(15Q11.2) WILD-TYPE 59 46 36 55 6

Figure S232.  Get High-res Image Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 37(15q11.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.09

Table S233.  Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 89 65 58
DEL PEAK 37(15Q11.2) MUTATED 10 59 33 17
DEL PEAK 37(15Q11.2) WILD-TYPE 13 30 32 41

Figure S233.  Get High-res Image Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 37(15q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.83e-09 (Chi-square test), Q value = 1.4e-06

Table S234.  Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 37(15Q11.2) MUTATED 69 27 11 51 21
DEL PEAK 37(15Q11.2) WILD-TYPE 29 48 43 30 23

Figure S234.  Get High-res Image Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 37(15q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-07 (Fisher's exact test), Q value = 7.6e-05

Table S235.  Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 37(15Q11.2) MUTATED 59 49 71
DEL PEAK 37(15Q11.2) WILD-TYPE 93 56 24

Figure S235.  Get High-res Image Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(15q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000156 (Fisher's exact test), Q value = 0.087

Table S236.  Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 37(15Q11.2) MUTATED 61 70 67
DEL PEAK 37(15Q11.2) WILD-TYPE 102 45 53

Figure S236.  Get High-res Image Gene #68: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 38(16q23.1) mutation analysis' versus 'CN_CNMF'

P value = 2.59e-07 (Fisher's exact test), Q value = 0.00018

Table S237.  Gene #69: 'Del Peak 38(16q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 38(16Q23.1) MUTATED 68 37 40 15
DEL PEAK 38(16Q23.1) WILD-TYPE 80 151 47 34

Figure S237.  Get High-res Image Gene #69: 'Del Peak 38(16q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 38(16q23.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00046 (Chi-square test), Q value = 0.24

Table S238.  Gene #69: 'Del Peak 38(16q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 38(16Q23.1) MUTATED 16 40 43 30 7
DEL PEAK 38(16Q23.1) WILD-TYPE 74 54 52 70 18

Figure S238.  Get High-res Image Gene #69: 'Del Peak 38(16q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 38(16q23.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.74e-07 (Chi-square test), Q value = 0.00019

Table S239.  Gene #69: 'Del Peak 38(16q23.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 38(16Q23.1) MUTATED 51 12 15 36 7
DEL PEAK 38(16Q23.1) WILD-TYPE 47 63 39 45 37

Figure S239.  Get High-res Image Gene #69: 'Del Peak 38(16q23.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 38(16q23.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.66e-08 (Fisher's exact test), Q value = 2.7e-05

Table S240.  Gene #69: 'Del Peak 38(16q23.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 38(16Q23.1) MUTATED 28 43 50
DEL PEAK 38(16Q23.1) WILD-TYPE 124 62 45

Figure S240.  Get High-res Image Gene #69: 'Del Peak 38(16q23.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(16q24.3) mutation analysis' versus 'CN_CNMF'

P value = 1.66e-06 (Fisher's exact test), Q value = 0.0011

Table S241.  Gene #70: 'Del Peak 39(16q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 39(16Q24.3) MUTATED 73 45 43 17
DEL PEAK 39(16Q24.3) WILD-TYPE 75 143 44 32

Figure S241.  Get High-res Image Gene #70: 'Del Peak 39(16q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 39(16q24.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.12e-06 (Chi-square test), Q value = 0.0014

Table S242.  Gene #70: 'Del Peak 39(16q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 39(16Q24.3) MUTATED 51 16 14 41 9
DEL PEAK 39(16Q24.3) WILD-TYPE 47 59 40 40 35

Figure S242.  Get High-res Image Gene #70: 'Del Peak 39(16q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 39(16q24.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.23e-06 (Fisher's exact test), Q value = 0.0021

Table S243.  Gene #70: 'Del Peak 39(16q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 39(16Q24.3) MUTATED 35 46 50
DEL PEAK 39(16Q24.3) WILD-TYPE 117 59 45

Figure S243.  Get High-res Image Gene #70: 'Del Peak 39(16q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(17p13.3) mutation analysis' versus 'CN_CNMF'

P value = 2.78e-13 (Fisher's exact test), Q value = 2.2e-10

Table S244.  Gene #71: 'Del Peak 40(17p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 40(17P13.3) MUTATED 111 63 53 25
DEL PEAK 40(17P13.3) WILD-TYPE 37 125 34 24

Figure S244.  Get High-res Image Gene #71: 'Del Peak 40(17p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 40(17p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.56e-08 (Chi-square test), Q value = 5.5e-05

Table S245.  Gene #71: 'Del Peak 40(17p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 40(17P13.3) MUTATED 29 51 69 44 19
DEL PEAK 40(17P13.3) WILD-TYPE 61 43 26 56 6

Figure S245.  Get High-res Image Gene #71: 'Del Peak 40(17p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 40(17p13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.83e-05 (Chi-square test), Q value = 0.039

Table S246.  Gene #71: 'Del Peak 40(17p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 40(17P13.3) MUTATED 72 29 28 52 22
DEL PEAK 40(17P13.3) WILD-TYPE 26 46 26 29 22

Figure S246.  Get High-res Image Gene #71: 'Del Peak 40(17p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 40(17p13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.38e-06 (Fisher's exact test), Q value = 0.004

Table S247.  Gene #71: 'Del Peak 40(17p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 40(17P13.3) MUTATED 67 65 71
DEL PEAK 40(17P13.3) WILD-TYPE 85 40 24

Figure S247.  Get High-res Image Gene #71: 'Del Peak 40(17p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(18q21.32) mutation analysis' versus 'CN_CNMF'

P value = 8.58e-10 (Fisher's exact test), Q value = 6.6e-07

Table S248.  Gene #72: 'Del Peak 41(18q21.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 41(18Q21.32) MUTATED 102 69 48 14
DEL PEAK 41(18Q21.32) WILD-TYPE 46 119 39 35

Figure S248.  Get High-res Image Gene #72: 'Del Peak 41(18q21.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 42(18q23) mutation analysis' versus 'CN_CNMF'

P value = 9.31e-13 (Fisher's exact test), Q value = 7.4e-10

Table S249.  Gene #73: 'Del Peak 42(18q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 42(18Q23) MUTATED 104 65 48 11
DEL PEAK 42(18Q23) WILD-TYPE 44 123 39 38

Figure S249.  Get High-res Image Gene #73: 'Del Peak 42(18q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 42(18q23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Chi-square test), Q value = 0.2

Table S250.  Gene #73: 'Del Peak 42(18q23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 42(18Q23) MUTATED 65 28 26 31 25
DEL PEAK 42(18Q23) WILD-TYPE 33 47 28 50 19

Figure S250.  Get High-res Image Gene #73: 'Del Peak 42(18q23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 2.6e-12 (Fisher's exact test), Q value = 2.1e-09

Table S251.  Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 43(19P13.3) MUTATED 77 69 70 36
DEL PEAK 43(19P13.3) WILD-TYPE 71 119 17 13

Figure S251.  Get High-res Image Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.35e-07 (Chi-square test), Q value = 0.00017

Table S252.  Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 43(19P13.3) MUTATED 38 73 41 46 18
DEL PEAK 43(19P13.3) WILD-TYPE 52 21 54 54 7

Figure S252.  Get High-res Image Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 2.15e-06 (Chi-square test), Q value = 0.0014

Table S253.  Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 43(19P13.3) MUTATED 49 34 34 63 14
DEL PEAK 43(19P13.3) WILD-TYPE 49 41 20 18 30

Figure S253.  Get High-res Image Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 1.9e-08 (Fisher's exact test), Q value = 1.4e-05

Table S254.  Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 43(19P13.3) MUTATED 61 81 52
DEL PEAK 43(19P13.3) WILD-TYPE 91 24 43

Figure S254.  Get High-res Image Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0016

Table S255.  Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 43(19P13.3) MUTATED 67 122 22
DEL PEAK 43(19P13.3) WILD-TYPE 91 61 35

Figure S255.  Get High-res Image Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 9.36e-06 (Fisher's exact test), Q value = 0.0058

Table S256.  Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 43(19P13.3) MUTATED 66 62 83
DEL PEAK 43(19P13.3) WILD-TYPE 97 53 37

Figure S256.  Get High-res Image Gene #74: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 44(19p13.2) mutation analysis' versus 'CN_CNMF'

P value = 1.25e-11 (Fisher's exact test), Q value = 9.9e-09

Table S257.  Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 44(19P13.2) MUTATED 77 66 66 37
DEL PEAK 44(19P13.2) WILD-TYPE 71 122 21 12

Figure S257.  Get High-res Image Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 44(19p13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.22e-08 (Chi-square test), Q value = 1.7e-05

Table S258.  Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 44(19P13.2) MUTATED 35 74 43 42 17
DEL PEAK 44(19P13.2) WILD-TYPE 55 20 52 58 8

Figure S258.  Get High-res Image Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 44(19p13.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.06e-06 (Chi-square test), Q value = 0.00071

Table S259.  Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 44(19P13.2) MUTATED 49 32 29 63 13
DEL PEAK 44(19P13.2) WILD-TYPE 49 43 25 18 31

Figure S259.  Get High-res Image Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 44(19p13.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.00085

Table S260.  Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 44(19P13.2) MUTATED 59 75 52
DEL PEAK 44(19P13.2) WILD-TYPE 93 30 43

Figure S260.  Get High-res Image Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 44(19p13.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.00098

Table S261.  Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 44(19P13.2) MUTATED 65 118 19
DEL PEAK 44(19P13.2) WILD-TYPE 93 65 38

Figure S261.  Get High-res Image Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 44(19p13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.99e-07 (Fisher's exact test), Q value = 0.00034

Table S262.  Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 44(19P13.2) MUTATED 62 56 84
DEL PEAK 44(19P13.2) WILD-TYPE 101 59 36

Figure S262.  Get High-res Image Gene #75: 'Del Peak 44(19p13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 45(19p12) mutation analysis' versus 'CN_CNMF'

P value = 9.72e-13 (Fisher's exact test), Q value = 7.7e-10

Table S263.  Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 45(19P12) MUTATED 75 41 55 28
DEL PEAK 45(19P12) WILD-TYPE 73 147 32 21

Figure S263.  Get High-res Image Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 45(19p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.71e-05 (Chi-square test), Q value = 0.01

Table S264.  Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 45(19P12) MUTATED 26 56 40 32 16
DEL PEAK 45(19P12) WILD-TYPE 64 38 55 68 9

Figure S264.  Get High-res Image Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 45(19p12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.24e-05 (Chi-square test), Q value = 0.047

Table S265.  Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 45(19P12) MUTATED 46 20 26 48 11
DEL PEAK 45(19P12) WILD-TYPE 52 55 28 33 33

Figure S265.  Get High-res Image Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 45(19p12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.88e-06 (Fisher's exact test), Q value = 0.0037

Table S266.  Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 45(19P12) MUTATED 43 59 49
DEL PEAK 45(19P12) WILD-TYPE 109 46 46

Figure S266.  Get High-res Image Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 45(19p12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.34e-05 (Fisher's exact test), Q value = 0.014

Table S267.  Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 45(19P12) MUTATED 49 97 16
DEL PEAK 45(19P12) WILD-TYPE 109 86 41

Figure S267.  Get High-res Image Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 45(19p12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.11

Table S268.  Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 45(19P12) MUTATED 48 50 64
DEL PEAK 45(19P12) WILD-TYPE 115 65 56

Figure S268.  Get High-res Image Gene #76: 'Del Peak 45(19p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 46(19q13.33) mutation analysis' versus 'CN_CNMF'

P value = 2.02e-07 (Fisher's exact test), Q value = 0.00014

Table S269.  Gene #77: 'Del Peak 46(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 46(19Q13.33) MUTATED 75 41 39 19
DEL PEAK 46(19Q13.33) WILD-TYPE 73 147 48 30

Figure S269.  Get High-res Image Gene #77: 'Del Peak 46(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 46(19q13.33) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000137 (Fisher's exact test), Q value = 0.077

Table S270.  Gene #77: 'Del Peak 46(19q13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 46(19Q13.33) MUTATED 38 84 21
DEL PEAK 46(19Q13.33) WILD-TYPE 120 99 36

Figure S270.  Get High-res Image Gene #77: 'Del Peak 46(19q13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 46(19q13.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0071

Table S271.  Gene #77: 'Del Peak 46(19q13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 46(19Q13.33) MUTATED 37 48 58
DEL PEAK 46(19Q13.33) WILD-TYPE 126 67 62

Figure S271.  Get High-res Image Gene #77: 'Del Peak 46(19q13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 47(20p13) mutation analysis' versus 'CN_CNMF'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0016

Table S272.  Gene #78: 'Del Peak 47(20p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 47(20P13) MUTATED 59 31 25 6
DEL PEAK 47(20P13) WILD-TYPE 89 157 62 43

Figure S272.  Get High-res Image Gene #78: 'Del Peak 47(20p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 48(21q11.2) mutation analysis' versus 'CN_CNMF'

P value = 3.1e-11 (Fisher's exact test), Q value = 2.4e-08

Table S273.  Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 48(21Q11.2) MUTATED 32 46 51 28
DEL PEAK 48(21Q11.2) WILD-TYPE 116 142 36 21

Figure S273.  Get High-res Image Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 48(21q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000131 (Chi-square test), Q value = 0.074

Table S274.  Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 48(21Q11.2) MUTATED 14 44 34 34 5
DEL PEAK 48(21Q11.2) WILD-TYPE 76 50 61 66 20

Figure S274.  Get High-res Image Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 48(21q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.83e-08 (Chi-square test), Q value = 6.4e-05

Table S275.  Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 48(21Q11.2) MUTATED 33 9 24 46 11
DEL PEAK 48(21Q11.2) WILD-TYPE 65 66 30 35 33

Figure S275.  Get High-res Image Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 48(21q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.62e-09 (Fisher's exact test), Q value = 3.5e-06

Table S276.  Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 48(21Q11.2) MUTATED 30 60 33
DEL PEAK 48(21Q11.2) WILD-TYPE 122 45 62

Figure S276.  Get High-res Image Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 48(21q11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.012

Table S277.  Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 48(21Q11.2) MUTATED 35 84 18
DEL PEAK 48(21Q11.2) WILD-TYPE 123 99 39

Figure S277.  Get High-res Image Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 48(21q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.83e-06 (Fisher's exact test), Q value = 0.0037

Table S278.  Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 48(21Q11.2) MUTATED 37 39 61
DEL PEAK 48(21Q11.2) WILD-TYPE 126 76 59

Figure S278.  Get High-res Image Gene #79: 'Del Peak 48(21q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 49(21q21.3) mutation analysis' versus 'CN_CNMF'

P value = 9.45e-11 (Fisher's exact test), Q value = 7.4e-08

Table S279.  Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 49(21Q21.3) MUTATED 32 44 49 28
DEL PEAK 49(21Q21.3) WILD-TYPE 116 144 38 21

Figure S279.  Get High-res Image Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 49(21q21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.28e-05 (Chi-square test), Q value = 0.0078

Table S280.  Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 49(21Q21.3) MUTATED 12 45 28 35 5
DEL PEAK 49(21Q21.3) WILD-TYPE 78 49 67 65 20

Figure S280.  Get High-res Image Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 49(21q21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.19e-10 (Chi-square test), Q value = 9.3e-08

Table S281.  Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 49(21Q21.3) MUTATED 28 9 24 51 10
DEL PEAK 49(21Q21.3) WILD-TYPE 70 66 30 30 34

Figure S281.  Get High-res Image Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 49(21q21.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.08e-12 (Fisher's exact test), Q value = 1.6e-09

Table S282.  Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 49(21Q21.3) MUTATED 27 65 30
DEL PEAK 49(21Q21.3) WILD-TYPE 125 40 65

Figure S282.  Get High-res Image Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 49(21q21.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.98e-05 (Fisher's exact test), Q value = 0.017

Table S283.  Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 49(21Q21.3) MUTATED 34 82 19
DEL PEAK 49(21Q21.3) WILD-TYPE 124 101 38

Figure S283.  Get High-res Image Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 49(21q21.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.38e-07 (Fisher's exact test), Q value = 0.00057

Table S284.  Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 49(21Q21.3) MUTATED 35 38 62
DEL PEAK 49(21Q21.3) WILD-TYPE 128 77 58

Figure S284.  Get High-res Image Gene #80: 'Del Peak 49(21q21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 50(22q13.32) mutation analysis' versus 'CN_CNMF'

P value = 6.18e-13 (Fisher's exact test), Q value = 4.9e-10

Table S285.  Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 50(22Q13.32) MUTATED 90 49 52 33
DEL PEAK 50(22Q13.32) WILD-TYPE 58 139 35 16

Figure S285.  Get High-res Image Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 50(22q13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.57e-08 (Chi-square test), Q value = 3.4e-05

Table S286.  Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 90 94 95 100 25
DEL PEAK 50(22Q13.32) MUTATED 20 58 57 41 15
DEL PEAK 50(22Q13.32) WILD-TYPE 70 36 38 59 10

Figure S286.  Get High-res Image Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 50(22q13.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.08e-09 (Chi-square test), Q value = 3.9e-06

Table S287.  Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 98 75 54 81 44
DEL PEAK 50(22Q13.32) MUTATED 55 22 26 58 9
DEL PEAK 50(22Q13.32) WILD-TYPE 43 53 28 23 35

Figure S287.  Get High-res Image Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 50(22q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.88e-09 (Fisher's exact test), Q value = 3.7e-06

Table S288.  Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 105 95
DEL PEAK 50(22Q13.32) MUTATED 46 71 53
DEL PEAK 50(22Q13.32) WILD-TYPE 106 34 42

Figure S288.  Get High-res Image Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 50(22q13.32) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.67e-05 (Fisher's exact test), Q value = 0.01

Table S289.  Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 183 57
DEL PEAK 50(22Q13.32) MUTATED 58 111 22
DEL PEAK 50(22Q13.32) WILD-TYPE 100 72 35

Figure S289.  Get High-res Image Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 50(22q13.32) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.76e-08 (Fisher's exact test), Q value = 2.8e-05

Table S290.  Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 115 120
DEL PEAK 50(22Q13.32) MUTATED 51 62 78
DEL PEAK 50(22Q13.32) WILD-TYPE 112 53 42

Figure S290.  Get High-res Image Gene #81: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 51(Xp22.2) mutation analysis' versus 'CN_CNMF'

P value = 1.99e-07 (Fisher's exact test), Q value = 0.00014

Table S291.  Gene #82: 'Del Peak 51(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 188 87 49
DEL PEAK 51(XP22.2) MUTATED 68 32 25 12
DEL PEAK 51(XP22.2) WILD-TYPE 80 156 62 37

Figure S291.  Get High-res Image Gene #82: 'Del Peak 51(Xp22.2) 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 = LUAD-TP.transferedmergedcluster.txt

  • Number of patients = 472

  • Number of copy number variation regions = 82

  • 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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