Correlation between copy number variation genes and molecular subtypes

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.

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)

[4] GISTIC_version2

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