Correlation between copy number variation genes and molecular subtypes

Lung Adenocarcinoma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C16Q1VFQ

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 77 peak regions and 10 molecular subtypes across 403 patients, 253 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' and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 4(3q26.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_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 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 9(6p25.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 10(6p21.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(7p21.1) cnvs correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 12(7p11.2) cnvs correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 13(7q31.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 14(8p11.21) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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(18p11.32) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 27(18q11.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 28(19q12) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 29(20q11.21) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 30(20q13.33) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 32(Xq28) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 1(1p36.13) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 2(1p13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 5(3p26.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 6(3p21.31) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 8(3q29) cnvs correlated to 'MRNASEQ_CNMF'.
Del Peak 9(4p15.2) cnvs correlated to '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 13(5q34) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 15(6q22.31) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 17(8p23.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 18(8p21.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 19(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 20(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 21(9q21.11) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 22(10p15.3) cnvs correlated to 'CN_CNMF'.
Del Peak 23(10q26.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(11p15.5) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 25(11q25) cnvs correlated to 'MRNASEQ_CNMF'.
Del Peak 28(12q24.33) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 29(13q12.11) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 30(13q12.13) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 31(13q34) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 33(15q11.2) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 34(15q15.3) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 35(16q23.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 36(17p13.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 37(18q21.32) cnvs correlated to 'CN_CNMF'.
Del Peak 38(18q23) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 39(19p13.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 40(19p13.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 41(19q11) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 42(19q13.33) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 43(21q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 44(22q13.32) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 45(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 77 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 253 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 4(3q26 2)	141 (35%)	262	0.000264 (0.14)	0.00332 (1.00)	1.34e-08 (9.45e-06)	1.27e-07 (8.58e-05)	0.000432 (0.225)	0.000718 (0.364)	1.11e-08 (7.89e-06)	3.47e-07 (0.000231)	8.66e-08 (5.93e-05)	9.8e-08 (6.69e-05)
Del Peak 10(4q22 1)	119 (30%)	284	0.000214 (0.114)	9.89e-05 (0.0544)	2.34e-06 (0.00147)	0.000345 (0.181)	0.129 (1.00)	0.0837 (1.00)	5.41e-07 (0.000355)	3.52e-12 (2.64e-09)	5.18e-07 (0.000341)	1.14e-08 (8.07e-06)
Amp Peak 12(7p11 2)	210 (52%)	193	1 (1.00)	1 (1.00)	4.33e-17 (3.3e-14)	0.00642 (1.00)	0.000351 (0.183)	0.000134 (0.0729)	5.63e-11 (4.17e-08)	4.07e-09 (2.92e-06)	2.3e-06 (0.00145)	1.05e-06 (0.000674)
Amp Peak 24(17q12)	180 (45%)	223	0.179 (1.00)	0.049 (1.00)	2.67e-12 (2e-09)	8.86e-07 (0.000576)	0.0598 (1.00)	6.42e-05 (0.0357)	1.05e-06 (0.000676)	6.71e-08 (4.65e-05)	3.19e-06 (0.00198)	1.01e-07 (6.86e-05)
Amp Peak 25(17q23 1)	195 (48%)	208	0.081 (1.00)	0.208 (1.00)	3.34e-13 (2.53e-10)	4.55e-06 (0.00279)	0.00118 (0.574)	8.12e-08 (5.58e-05)	1.84e-07 (0.000124)	2.9e-10 (2.13e-07)	1.71e-05 (0.00978)	5.39e-06 (0.00327)
Del Peak 13(5q34)	140 (35%)	263	0.0545 (1.00)	0.157 (1.00)	5.72e-13 (4.31e-10)	2.05e-08 (1.44e-05)	0.0102 (1.00)	0.000302 (0.159)	9.81e-07 (0.000633)	8.33e-11 (6.16e-08)	1.38e-10 (1.02e-07)	3.78e-10 (2.78e-07)
Del Peak 43(21q11 2)	140 (35%)	263	0.0604 (1.00)	0.0501 (1.00)	4.23e-08 (2.95e-05)	3.11e-05 (0.0176)	0.00283 (1.00)	7.72e-05 (0.0429)	8.83e-08 (6.04e-05)	4.62e-09 (3.31e-06)	1.98e-05 (0.0113)	5.83e-06 (0.00351)
Amp Peak 11(7p21 1)	220 (55%)	183	0.743 (1.00)	1 (1.00)	9.54e-19 (7.34e-16)	0.0107 (1.00)	0.000437 (0.227)	0.0006 (0.308)	7.98e-08 (5.49e-05)	2.31e-08 (1.62e-05)	0.00021 (0.112)	0.000238 (0.126)
Amp Peak 15(8q11 1)	182 (45%)	221	0.00472 (1.00)	0.0134 (1.00)	1.32e-11 (9.86e-09)	2.16e-05 (0.0124)	0.0189 (1.00)	0.00193 (0.907)	4.21e-06 (0.00259)	2.93e-05 (0.0167)	3.26e-07 (0.000218)	4.91e-06 (0.003)
Amp Peak 16(8q24 21)	251 (62%)	152	0.00707 (1.00)	0.0109 (1.00)	3.49e-13 (2.63e-10)	7.75e-08 (5.35e-05)	0.133 (1.00)	0.00406 (1.00)	6.41e-07 (0.000418)	9.15e-05 (0.0504)	6.21e-07 (0.000406)	6.85e-07 (0.000447)
Amp Peak 18(11q13 3)	137 (34%)	266	0.00118 (0.575)	0.000736 (0.369)	2.2e-13 (1.67e-10)	7.27e-06 (0.00435)	0.0108 (1.00)	0.00335 (1.00)	3.18e-05 (0.018)	3.55e-07 (0.000236)	4.77e-08 (3.33e-05)	8.56e-08 (5.87e-05)
Amp Peak 19(12p12 1)	140 (35%)	263	0.198 (1.00)	0.033 (1.00)	1.72e-17 (1.32e-14)	1.78e-07 (0.00012)	0.0147 (1.00)	0.0511 (1.00)	9.69e-07 (0.000627)	3.96e-06 (0.00244)	1.04e-05 (0.00609)	7.46e-06 (0.00445)
Amp Peak 20(12q14 1)	125 (31%)	278	0.406 (1.00)	0.302 (1.00)	7.88e-18 (6.04e-15)	1.06e-05 (0.00616)	0.0146 (1.00)	0.00348 (1.00)	2.68e-07 (0.000179)	2.26e-09 (1.63e-06)	2.63e-08 (1.84e-05)	9.79e-09 (6.95e-06)
Amp Peak 21(12q15)	129 (32%)	274	0.221 (1.00)	0.103 (1.00)	6.32e-15 (4.8e-12)	2.77e-06 (0.00173)	0.0176 (1.00)	0.00257 (1.00)	4.86e-07 (0.000321)	2.18e-07 (0.000146)	1.92e-07 (0.000129)	3.98e-09 (2.86e-06)
Amp Peak 23(14q13 3)	180 (45%)	223	0.562 (1.00)	0.254 (1.00)	2.05e-10 (1.51e-07)	1.28e-05 (0.00742)	0.00644 (1.00)	0.0106 (1.00)	2.55e-10 (1.88e-07)	5.25e-05 (0.0294)	2.37e-06 (0.00149)	3.6e-09 (2.6e-06)
Del Peak 11(4q35 1)	143 (35%)	260	0.00204 (0.952)	0.00118 (0.575)	2.47e-09 (1.79e-06)	1.61e-08 (1.13e-05)	0.0232 (1.00)	0.000656 (0.334)	2.07e-11 (1.54e-08)	7.71e-17 (5.87e-14)	1.07e-08 (7.58e-06)	1.67e-14 (1.27e-11)
Del Peak 29(13q12 11)	225 (56%)	178	0.00113 (0.555)	0.0134 (1.00)	1.92e-16 (1.46e-13)	0.0145 (1.00)	0.0027 (1.00)	3.86e-06 (0.00238)	2.36e-06 (0.00148)	3.99e-09 (2.87e-06)	7.35e-06 (0.00439)	8.66e-07 (0.000564)
Del Peak 30(13q12 13)	224 (56%)	179	0.00862 (1.00)	0.0218 (1.00)	3.49e-18 (2.68e-15)	0.00153 (0.73)	0.000719 (0.364)	1.92e-06 (0.00121)	4.8e-06 (0.00294)	8.61e-09 (6.12e-06)	3.21e-05 (0.0181)	3.52e-06 (0.00218)
Del Peak 34(15q15 3)	205 (51%)	198	0.0816 (1.00)	0.0822 (1.00)	1.47e-12 (1.11e-09)	0.0019 (0.895)	0.112 (1.00)	3.26e-06 (0.00202)	8.87e-10 (6.45e-07)	6.32e-08 (4.38e-05)	0.000107 (0.0587)	5.31e-07 (0.000349)
Del Peak 44(22q13 32)	194 (48%)	209	0.0692 (1.00)	0.0871 (1.00)	1.3e-12 (9.8e-10)	6.77e-08 (4.68e-05)	0.00774 (1.00)	0.0352 (1.00)	5.08e-09 (3.62e-06)	4.88e-09 (3.48e-06)	1.67e-05 (0.00957)	3.76e-08 (2.63e-05)
Amp Peak 17(10p15 1)	108 (27%)	295	0.023 (1.00)	0.0262 (1.00)	9.73e-07 (0.000629)	2.39e-07 (0.00016)	0.00498 (1.00)	0.0094 (1.00)	0.00022 (0.117)	2.26e-06 (0.00142)	0.000724 (0.365)	0.000175 (0.0945)
Del Peak 9(4p15 2)	95 (24%)	308	0.595 (1.00)	0.453 (1.00)	0.00433 (1.00)	0.000106 (0.0579)	0.133 (1.00)	0.1 (1.00)	5.73e-06 (0.00346)	3.99e-07 (0.000265)	2.18e-06 (0.00138)	1.32e-06 (0.000844)
Del Peak 12(5q11 2)	145 (36%)	258	0.26 (1.00)	0.254 (1.00)	1.74e-11 (1.3e-08)	0.000894 (0.444)	0.00425 (1.00)	0.00833 (1.00)	1.01e-05 (0.00593)	7.77e-08 (5.36e-05)	4.54e-07 (0.000301)	7.44e-08 (5.14e-05)
Del Peak 18(8p21 3)	210 (52%)	193	0.00526 (1.00)	0.00382 (1.00)	2.24e-17 (1.72e-14)	0.00266 (1.00)	0.016 (1.00)	0.00102 (0.503)	5.06e-06 (0.00308)	1.93e-07 (0.000129)	0.000303 (0.159)	9.16e-07 (0.000593)
Del Peak 31(13q34)	183 (45%)	220	0.0356 (1.00)	0.0445 (1.00)	4.14e-10 (3.04e-07)	0.221 (1.00)	0.00336 (1.00)	0.000366 (0.191)	3.88e-05 (0.0219)	5.1e-06 (0.00309)	0.00145 (0.692)	0.000248 (0.131)
Del Peak 33(15q11 2)	200 (50%)	203	0.168 (1.00)	0.157 (1.00)	3.27e-11 (2.42e-08)	0.00969 (1.00)	0.212 (1.00)	0.000177 (0.0954)	1.83e-09 (1.33e-06)	1.05e-07 (7.17e-05)	0.00188 (0.883)	0.000156 (0.0847)
Del Peak 39(19p13 3)	216 (54%)	187	0.572 (1.00)	0.665 (1.00)	4.38e-10 (3.2e-07)	0.0868 (1.00)	0.459 (1.00)	0.359 (1.00)	2.15e-06 (0.00136)	1.9e-08 (1.34e-05)	2.4e-06 (0.0015)	9.36e-06 (0.00554)
Del Peak 40(19p13 2)	207 (51%)	196	0.694 (1.00)	1 (1.00)	7.84e-10 (5.71e-07)	0.0165 (1.00)	0.296 (1.00)	0.172 (1.00)	1.06e-06 (0.000683)	1.28e-06 (0.000818)	1.47e-06 (0.000936)	4.99e-07 (0.000329)
Amp Peak 28(19q12)	110 (27%)	293	0.0514 (1.00)	0.0219 (1.00)	3.41e-07 (0.000227)	0.103 (1.00)	0.0312 (1.00)	0.0592 (1.00)	0.00105 (0.515)	4.57e-05 (0.0257)	1.36e-06 (0.000866)	5.18e-07 (0.000341)
Amp Peak 30(20q13 33)	195 (48%)	208	0.00559 (1.00)	0.0301 (1.00)	4.75e-09 (3.4e-06)	0.0607 (1.00)	0.0071 (1.00)	0.00629 (1.00)	1.15e-05 (0.00668)	0.00467 (1.00)	1.02e-05 (0.006)	1.34e-05 (0.00772)
Del Peak 1(1p36 13)	92 (23%)	311	0.795 (1.00)	0.441 (1.00)	5.69e-07 (0.000373)	0.00217 (1.00)	0.42 (1.00)	0.447 (1.00)	5.33e-05 (0.0298)	0.000179 (0.0964)	0.000215 (0.115)	0.00724 (1.00)
Del Peak 5(3p26 3)	183 (45%)	220	0.0936 (1.00)	0.199 (1.00)	7.07e-06 (0.00423)	0.162 (1.00)	0.251 (1.00)	0.0574 (1.00)	0.133 (1.00)	3.14e-06 (0.00195)	0.000162 (0.0874)	5.54e-06 (0.00335)
Del Peak 6(3p21 31)	194 (48%)	209	0.132 (1.00)	0.478 (1.00)	9.12e-07 (0.000592)	0.141 (1.00)	0.036 (1.00)	0.0174 (1.00)	0.0189 (1.00)	3.35e-09 (2.42e-06)	8.43e-06 (0.005)	3e-06 (0.00187)
Del Peak 17(8p23 2)	197 (49%)	206	0.00526 (1.00)	0.00382 (1.00)	3.89e-17 (2.97e-14)	0.0102 (1.00)	0.0138 (1.00)	0.00138 (0.661)	1.05e-05 (0.00615)	1.83e-07 (0.000123)	0.00425 (1.00)	1.67e-06 (0.00106)
Amp Peak 8(5q35 1)	91 (23%)	312	0.0862 (1.00)	0.453 (1.00)	8.42e-05 (0.0467)	1.59e-05 (0.00914)	0.164 (1.00)	0.0546 (1.00)	0.0014 (0.669)	0.000153 (0.0833)	0.00108 (0.532)	0.0233 (1.00)
Amp Peak 13(7q31 2)	172 (43%)	231	0.482 (1.00)	0.429 (1.00)	6.81e-10 (4.97e-07)	0.0957 (1.00)	0.0903 (1.00)	0.0296 (1.00)	1.03e-09 (7.46e-07)	1.03e-07 (7.02e-05)	0.00659 (1.00)	0.00076 (0.38)
Amp Peak 14(8p11 21)	123 (31%)	280	0.256 (1.00)	0.453 (1.00)	7.62e-10 (5.55e-07)	0.00837 (1.00)	0.00772 (1.00)	0.00536 (1.00)	9.9e-06 (0.00584)	1.26e-07 (8.54e-05)	0.000861 (0.429)	0.00291 (1.00)
Amp Peak 29(20q11 21)	180 (45%)	223	0.0118 (1.00)	0.0337 (1.00)	4.67e-10 (3.41e-07)	0.0265 (1.00)	0.0209 (1.00)	0.00459 (1.00)	0.00333 (1.00)	0.0693 (1.00)	6.72e-06 (0.00403)	6.38e-05 (0.0356)
Del Peak 21(9q21 11)	202 (50%)	201	0.0335 (1.00)	0.597 (1.00)	1.04e-05 (0.00609)	0.129 (1.00)	0.106 (1.00)	0.0201 (1.00)	0.00567 (1.00)	9.41e-06 (0.00556)	0.00495 (1.00)	1.2e-05 (0.00696)
Del Peak 35(16q23 3)	145 (36%)	258	0.16 (1.00)	0.631 (1.00)	2.33e-05 (0.0133)	0.0178 (1.00)	0.018 (1.00)	0.059 (1.00)	5.06e-06 (0.00308)	2.77e-06 (0.00173)	0.0186 (1.00)	0.00269 (1.00)
Del Peak 36(17p13 3)	223 (55%)	180	0.386 (1.00)	0.609 (1.00)	1.11e-11 (8.33e-09)	0.000727 (0.365)	0.0459 (1.00)	0.00225 (1.00)	6.83e-05 (0.038)	6.38e-06 (0.00384)	0.00541 (1.00)	0.00352 (1.00)
Del Peak 42(19q13 33)	147 (36%)	256	0.272 (1.00)	0.383 (1.00)	1.13e-06 (0.000724)	0.196 (1.00)	0.151 (1.00)	0.512 (1.00)	0.0782 (1.00)	0.00945 (1.00)	0.000137 (0.0745)	1.17e-05 (0.0068)
Amp Peak 3(1q21 3)	285 (71%)	118	0.362 (1.00)	0.465 (1.00)	1.08e-05 (0.00632)	0.000726 (0.365)	0.416 (1.00)	0.568 (1.00)	0.203 (1.00)	0.866 (1.00)	0.0202 (1.00)	0.000116 (0.0637)
Amp Peak 6(5p15 33)	260 (65%)	143	0.878 (1.00)	0.901 (1.00)	3.24e-20 (2.5e-17)	0.94 (1.00)	0.0517 (1.00)	0.000555 (0.286)	1.29e-07 (8.74e-05)	0.00324 (1.00)	0.00357 (1.00)	0.00213 (0.993)
Amp Peak 7(5p13 1)	235 (58%)	168	0.263 (1.00)	0.897 (1.00)	3.08e-15 (2.34e-12)	1 (1.00)	0.387 (1.00)	0.0265 (1.00)	4.66e-06 (0.00285)	0.1 (1.00)	0.00294 (1.00)	0.0126 (1.00)
Amp Peak 9(6p25 3)	159 (39%)	244	0.487 (1.00)	0.157 (1.00)	1.63e-11 (1.22e-08)	0.00695 (1.00)	0.00388 (1.00)	0.108 (1.00)	6.19e-05 (0.0346)	0.327 (1.00)	0.0104 (1.00)	0.000785 (0.392)
Amp Peak 26(18p11 32)	103 (26%)	300	0.63 (1.00)	1 (1.00)	5.64e-08 (3.92e-05)	0.00224 (1.00)	0.228 (1.00)	0.47 (1.00)	0.00956 (1.00)	0.00798 (1.00)	0.000599 (0.308)	7.5e-06 (0.00446)
Amp Peak 27(18q11 2)	87 (22%)	316	0.195 (1.00)	0.0151 (1.00)	7.99e-06 (0.00475)	0.00822 (1.00)	0.0494 (1.00)	0.00362 (1.00)	0.0121 (1.00)	0.00315 (1.00)	0.00265 (1.00)	1.45e-06 (0.00092)
Amp Peak 32(Xq28)	130 (32%)	273	0.301 (1.00)	0.123 (1.00)	2.57e-12 (1.93e-09)	0.000895 (0.444)	0.0139 (1.00)	0.0234 (1.00)	0.000272 (0.143)	0.00287 (1.00)	0.0264 (1.00)	0.0338 (1.00)
Del Peak 24(11p15 5)	107 (27%)	296	0.268 (1.00)	0.0576 (1.00)	0.000126 (0.0687)	0.0159 (1.00)	0.00126 (0.61)	0.00535 (1.00)	0.00337 (1.00)	4.98e-06 (0.00304)	0.0056 (1.00)	0.00168 (0.792)
Del Peak 28(12q24 33)	95 (24%)	308	0.063 (1.00)	0.0396 (1.00)	8.61e-05 (0.0476)	0.113 (1.00)	0.0188 (1.00)	0.00155 (0.737)	0.00995 (1.00)	0.00104 (0.511)	0.00405 (1.00)	5.84e-06 (0.00351)
Del Peak 38(18q23)	196 (49%)	207	0.029 (1.00)	0.0968 (1.00)	1.2e-09 (8.66e-07)	0.809 (1.00)	0.00788 (1.00)	0.00362 (1.00)	0.00038 (0.198)	0.000628 (0.322)	0.0133 (1.00)	0.00274 (1.00)
Del Peak 41(19q11)	114 (28%)	289	0.951 (1.00)	0.539 (1.00)	1.68e-05 (0.00966)	0.209 (1.00)	0.0931 (1.00)	0.0839 (1.00)	0.00681 (1.00)	0.000213 (0.114)	0.00395 (1.00)	0.00243 (1.00)
Amp Peak 1(1p34 3)	111 (28%)	292	0.553 (1.00)	0.384 (1.00)	2.12e-12 (1.6e-09)	0.921 (1.00)	0.171 (1.00)	0.0842 (1.00)	0.0237 (1.00)	0.0591 (1.00)	0.241 (1.00)	0.708 (1.00)
Amp Peak 2(1p22 3)	106 (26%)	297	0.876 (1.00)	1 (1.00)	4.18e-10 (3.06e-07)	0.649 (1.00)	0.225 (1.00)	0.281 (1.00)	0.0527 (1.00)	0.00703 (1.00)	0.434 (1.00)	0.108 (1.00)
Amp Peak 5(4q12)	76 (19%)	327	0.703 (1.00)	0.206 (1.00)	1.81e-08 (1.28e-05)	0.799 (1.00)	0.0222 (1.00)	0.0336 (1.00)	0.0725 (1.00)	0.00728 (1.00)	0.0228 (1.00)	0.00489 (1.00)
Amp Peak 10(6p21 1)	151 (37%)	252	0.675 (1.00)	0.206 (1.00)	5.34e-08 (3.72e-05)	0.0191 (1.00)	0.109 (1.00)	0.743 (1.00)	0.0298 (1.00)	0.94 (1.00)	0.15 (1.00)	0.0242 (1.00)
Del Peak 2(1p13 1)	119 (30%)	284	0.703 (1.00)	0.707 (1.00)	4.47e-05 (0.0252)	0.000563 (0.29)	0.227 (1.00)	0.609 (1.00)	0.00112 (0.547)	0.00669 (1.00)	0.00827 (1.00)	0.014 (1.00)
Del Peak 8(3q29)	112 (28%)	291	0.71 (1.00)	0.602 (1.00)	0.285 (1.00)	0.000681 (0.345)	0.0044 (1.00)	0.0209 (1.00)	8.83e-05 (0.0487)	0.0732 (1.00)	0.637 (1.00)	0.0249 (1.00)
Del Peak 15(6q22 31)	199 (49%)	204	0.54 (1.00)	0.187 (1.00)	0.095 (1.00)	0.00025 (0.133)	0.442 (1.00)	0.0275 (1.00)	0.055 (1.00)	0.981 (1.00)	0.374 (1.00)	0.527 (1.00)
Del Peak 19(9p23)	226 (56%)	177	0.521 (1.00)	0.901 (1.00)	0.000157 (0.085)	0.817 (1.00)	0.703 (1.00)	0.644 (1.00)	0.0572 (1.00)	0.0222 (1.00)	0.469 (1.00)	0.153 (1.00)
Del Peak 20(9p21 3)	232 (58%)	171	0.521 (1.00)	0.901 (1.00)	2.89e-05 (0.0165)	0.293 (1.00)	0.449 (1.00)	0.4 (1.00)	0.00457 (1.00)	0.013 (1.00)	0.826 (1.00)	0.204 (1.00)
Del Peak 22(10p15 3)	99 (25%)	304	1 (1.00)	1 (1.00)	2.69e-06 (0.00168)	0.381 (1.00)	0.575 (1.00)	0.671 (1.00)	0.00438 (1.00)	0.476 (1.00)	0.002 (0.937)	0.0227 (1.00)
Del Peak 23(10q26 3)	113 (28%)	290	0.748 (1.00)	0.283 (1.00)	1.14e-05 (0.00663)	0.19 (1.00)	0.00145 (0.692)	0.0123 (1.00)	0.000653 (0.333)	0.0171 (1.00)	0.0196 (1.00)	0.00601 (1.00)
Del Peak 25(11q25)	88 (22%)	315	0.108 (1.00)	0.0799 (1.00)	0.0215 (1.00)	0.302 (1.00)	0.000636 (0.325)	0.00462 (1.00)	0.000464 (0.24)	0.00596 (1.00)	0.114 (1.00)	0.433 (1.00)
Del Peak 37(18q21 32)	201 (50%)	202	0.115 (1.00)	0.227 (1.00)	8.39e-09 (5.98e-06)	0.701 (1.00)	0.00316 (1.00)	0.00593 (1.00)	0.00455 (1.00)	0.0109 (1.00)	0.0409 (1.00)	0.0217 (1.00)
Del Peak 45(Xp22 2)	117 (29%)	286	0.691 (1.00)	0.896 (1.00)	3.83e-07 (0.000254)	0.0269 (1.00)	0.0418 (1.00)	0.0764 (1.00)	0.000668 (0.339)	0.00124 (0.601)	0.544 (1.00)	0.514 (1.00)
Amp Peak 22(13q33 3)	62 (15%)	341	0.172 (1.00)	0.105 (1.00)	0.303 (1.00)	0.387 (1.00)	0.562 (1.00)	0.42 (1.00)	0.917 (1.00)	0.267 (1.00)	0.27 (1.00)	0.0982 (1.00)
Amp Peak 31(22q11 22)	69 (17%)	334	0.268 (1.00)	0.162 (1.00)	0.00488 (1.00)	0.26 (1.00)	0.0254 (1.00)	0.182 (1.00)	0.474 (1.00)	0.222 (1.00)	0.0605 (1.00)	0.0982 (1.00)
Del Peak 3(2q22 1)	41 (10%)	362	0.869 (1.00)	0.78 (1.00)	0.0073 (1.00)	0.576 (1.00)	0.0529 (1.00)	0.51 (1.00)	0.0542 (1.00)	0.00242 (1.00)	0.0476 (1.00)	0.121 (1.00)
Del Peak 4(2q37 3)	59 (15%)	344	0.703 (1.00)	0.206 (1.00)	0.00549 (1.00)	0.149 (1.00)	0.185 (1.00)	0.117 (1.00)	0.0125 (1.00)	0.00267 (1.00)	0.00448 (1.00)	0.0013 (0.625)
Del Peak 7(3q11 1)	116 (29%)	287	0.609 (1.00)	0.602 (1.00)	0.113 (1.00)	0.369 (1.00)	0.353 (1.00)	0.261 (1.00)	0.168 (1.00)	0.0277 (1.00)	0.856 (1.00)	0.728 (1.00)
Del Peak 14(6q12)	137 (34%)	266	0.532 (1.00)	1 (1.00)	0.843 (1.00)	0.17 (1.00)	0.427 (1.00)	0.142 (1.00)	0.882 (1.00)	0.928 (1.00)	0.172 (1.00)	0.005 (1.00)
Del Peak 16(6q26)	204 (51%)	199	0.368 (1.00)	0.276 (1.00)	0.0961 (1.00)	0.00175 (0.828)	0.411 (1.00)	0.00535 (1.00)	0.226 (1.00)	0.635 (1.00)	0.18 (1.00)	0.106 (1.00)
Del Peak 26(12p13 2)	107 (27%)	296	0.255 (1.00)	0.719 (1.00)	0.000946 (0.468)	0.00128 (0.618)	0.0581 (1.00)	0.00167 (0.79)	0.0202 (1.00)	0.0639 (1.00)	1 (1.00)	0.978 (1.00)
Del Peak 27(12q12)	77 (19%)	326	0.597 (1.00)	0.644 (1.00)	0.000495 (0.256)	0.317 (1.00)	0.0905 (1.00)	0.0113 (1.00)	0.0399 (1.00)	0.184 (1.00)	0.199 (1.00)	0.0222 (1.00)
Del Peak 32(14q32 33)	120 (30%)	283	0.703 (1.00)	0.302 (1.00)	0.00133 (0.638)	0.35 (1.00)	0.173 (1.00)	0.1 (1.00)	0.389 (1.00)	0.0751 (1.00)	0.0197 (1.00)	0.186 (1.00)

'Amp Peak 1(1p34.3) mutation analysis' versus 'CN_CNMF'

P value = 2.12e-12 (Fisher's exact test), Q value = 1.6e-09

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	122	157	70	54
AMP PEAK 1(1P34.3) MUTATED	64	20	18	9
AMP PEAK 1(1P34.3) WILD-TYPE	58	137	52	45

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 = 4.18e-10 (Fisher's exact test), Q value = 3.1e-07

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	122	157	70	54
AMP PEAK 2(1P22.3) MUTATED	58	18	17	13
AMP PEAK 2(1P22.3) WILD-TYPE	64	139	53	41

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 = 1.08e-05 (Fisher's exact test), Q value = 0.0063

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	122	157	70	54
AMP PEAK 3(1Q21.3) MUTATED	94	90	53	48
AMP PEAK 3(1Q21.3) WILD-TYPE	28	67	17	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 'MIRSEQ_CHIERARCHICAL'

P value = 0.000116 (Fisher's exact test), Q value = 0.064

Table S4. 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 S4. 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 S5. 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 S5. 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 = 1.34e-08 (Fisher's exact test), Q value = 9.4e-06

Table S6. 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	122	157	70	54
AMP PEAK 4(3Q26.2) MUTATED	43	33	45	20
AMP PEAK 4(3Q26.2) WILD-TYPE	79	124	25	34

Figure S6. 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 = 1.27e-07 (Fisher's exact test), Q value = 8.6e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 4(3Q26.2) MUTATED	8	46	51
AMP PEAK 4(3Q26.2) WILD-TYPE	70	66	61

Figure S7. 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 'RPPA_CNMF'

P value = 0.000432 (Fisher's exact test), Q value = 0.22

Table S8. Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	75	71
AMP PEAK 4(3Q26.2) MUTATED	36	16	37
AMP PEAK 4(3Q26.2) WILD-TYPE	53	59	34

Figure S8. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 1.11e-08 (Chi-square test), Q value = 7.9e-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 = 0.00023

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 = 5.9e-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 = 6.7e-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 = 1.81e-08 (Fisher's exact test), Q value = 1.3e-05

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	122	157	70	54
AMP PEAK 5(4Q12) MUTATED	38	8	17	13
AMP PEAK 5(4Q12) WILD-TYPE	84	149	53	41

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 = 3.24e-20 (Fisher's exact test), Q value = 2.5e-17

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	122	157	70	54
AMP PEAK 6(5P15.33) MUTATED	112	65	39	44
AMP PEAK 6(5P15.33) WILD-TYPE	10	92	31	10

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 = 8.7e-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 = 3.08e-15 (Fisher's exact test), Q value = 2.3e-12

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	122	157	70	54
AMP PEAK 7(5P13.1) MUTATED	101	59	34	41
AMP PEAK 7(5P13.1) WILD-TYPE	21	98	36	13

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 = 4.66e-06 (Chi-square test), Q value = 0.0029

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	16	54	28
AMP PEAK 7(5P13.1) WILD-TYPE	29	39	38	27	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 'CN_CNMF'

P value = 8.42e-05 (Fisher's exact test), Q value = 0.047

Table S18. Gene #8: 'Amp Peak 8(5q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 8(5Q35.1) MUTATED	42	35	5	9
AMP PEAK 8(5Q35.1) WILD-TYPE	80	122	65	45

Figure S18. Get High-res Image Gene #8: 'Amp Peak 8(5q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.59e-05 (Fisher's exact test), Q value = 0.0091

Table S19. Gene #8: 'Amp Peak 8(5q35.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 8(5Q35.1) MUTATED	35	18	21
AMP PEAK 8(5Q35.1) WILD-TYPE	43	94	91

Figure S19. 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 = 0.083

Table S20. 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 S20. Get High-res Image Gene #8: 'Amp Peak 8(5q35.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 9(6p25.3) mutation analysis' versus 'CN_CNMF'

P value = 1.63e-11 (Fisher's exact test), Q value = 1.2e-08

Table S21. Gene #9: 'Amp Peak 9(6p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 9(6P25.3) MUTATED	47	38	31	43
AMP PEAK 9(6P25.3) WILD-TYPE	75	119	39	11

Figure S21. Get High-res Image Gene #9: 'Amp Peak 9(6p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 9(6p25.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.19e-05 (Chi-square test), Q value = 0.035

Table S22. Gene #9: 'Amp Peak 9(6p25.3) 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 9(6P25.3) MUTATED	33	30	11	49	17
AMP PEAK 9(6P25.3) WILD-TYPE	65	45	43	32	27

Figure S22. Get High-res Image Gene #9: 'Amp Peak 9(6p25.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 10(6p21.1) mutation analysis' versus 'CN_CNMF'

P value = 5.34e-08 (Fisher's exact test), Q value = 3.7e-05

Table S23. Gene #10: 'Amp Peak 10(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 10(6P21.1) MUTATED	48	38	27	38
AMP PEAK 10(6P21.1) WILD-TYPE	74	119	43	16

Figure S23. Get High-res Image Gene #10: 'Amp Peak 10(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 11(7p21.1) mutation analysis' versus 'CN_CNMF'

P value = 9.54e-19 (Fisher's exact test), Q value = 7.3e-16

Table S24. Gene #11: 'Amp Peak 11(7p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 11(7P21.1) MUTATED	104	50	41	25
AMP PEAK 11(7P21.1) WILD-TYPE	18	107	29	29

Figure S24. Get High-res Image Gene #11: 'Amp Peak 11(7p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 11(7p21.1) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000437 (Fisher's exact test), Q value = 0.23

Table S25. Gene #11: 'Amp Peak 11(7p21.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	75	71
AMP PEAK 11(7P21.1) MUTATED	61	29	43
AMP PEAK 11(7P21.1) WILD-TYPE	28	46	28

Figure S25. Get High-res Image Gene #11: 'Amp Peak 11(7p21.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 11(7p21.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.98e-08 (Chi-square test), Q value = 5.5e-05

Table S26. Gene #11: 'Amp Peak 11(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 11(7P21.1) MUTATED	76	24	27	41	28
AMP PEAK 11(7P21.1) WILD-TYPE	22	51	27	40	16

Figure S26. Get High-res Image Gene #11: 'Amp Peak 11(7p21.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 11(7p21.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.31e-08 (Fisher's exact test), Q value = 1.6e-05

Table S27. Gene #11: 'Amp Peak 11(7p21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
AMP PEAK 11(7P21.1) MUTATED	65	55	76
AMP PEAK 11(7P21.1) WILD-TYPE	87	50	19

Figure S27. Get High-res Image Gene #11: 'Amp Peak 11(7p21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(7p21.1) mutation analysis' versus 'MIRSEQ_CNMF'

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

Table S28. Gene #11: 'Amp Peak 11(7p21.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
AMP PEAK 11(7P21.1) MUTATED	68	108	41
AMP PEAK 11(7P21.1) WILD-TYPE	90	75	16

Figure S28. Get High-res Image Gene #11: 'Amp Peak 11(7p21.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 11(7p21.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S29. Gene #11: 'Amp Peak 11(7p21.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
AMP PEAK 11(7P21.1) MUTATED	70	77	70
AMP PEAK 11(7P21.1) WILD-TYPE	93	38	50

Figure S29. Get High-res Image Gene #11: 'Amp Peak 11(7p21.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 12(7p11.2) mutation analysis' versus 'CN_CNMF'

P value = 4.33e-17 (Fisher's exact test), Q value = 3.3e-14

Table S30. Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 12(7P11.2) MUTATED	99	49	42	20
AMP PEAK 12(7P11.2) WILD-TYPE	23	108	28	34

Figure S30. Get High-res Image Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 12(7p11.2) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000351 (Fisher's exact test), Q value = 0.18

Table S31. Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	75	71
AMP PEAK 12(7P11.2) MUTATED	58	27	44
AMP PEAK 12(7P11.2) WILD-TYPE	31	48	27

Figure S31. Get High-res Image Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 12(7p11.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000134 (Fisher's exact test), Q value = 0.073

Table S32. Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	73	83	56
AMP PEAK 12(7P11.2) MUTATED	7	43	58	21
AMP PEAK 12(7P11.2) WILD-TYPE	16	30	25	35

Figure S32. Get High-res Image Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 12(7p11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.63e-11 (Chi-square test), Q value = 4.2e-08

Table S33. Gene #12: 'Amp Peak 12(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 12(7P11.2) MUTATED	76	17	28	38	27
AMP PEAK 12(7P11.2) WILD-TYPE	22	58	26	43	17

Figure S33. Get High-res Image Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 12(7p11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.07e-09 (Fisher's exact test), Q value = 2.9e-06

Table S34. Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
AMP PEAK 12(7P11.2) MUTATED	58	54	74
AMP PEAK 12(7P11.2) WILD-TYPE	94	51	21

Figure S34. Get High-res Image Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(7p11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.3e-06 (Fisher's exact test), Q value = 0.0014

Table S35. Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
AMP PEAK 12(7P11.2) MUTATED	59	107	41
AMP PEAK 12(7P11.2) WILD-TYPE	99	76	16

Figure S35. Get High-res Image Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 12(7p11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00067

Table S36. Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
AMP PEAK 12(7P11.2) MUTATED	62	80	65
AMP PEAK 12(7P11.2) WILD-TYPE	101	35	55

Figure S36. Get High-res Image Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 13(7q31.2) mutation analysis' versus 'CN_CNMF'

P value = 6.81e-10 (Fisher's exact test), Q value = 5e-07

Table S37. Gene #13: 'Amp Peak 13(7q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 13(7Q31.2) MUTATED	81	42	29	20
AMP PEAK 13(7Q31.2) WILD-TYPE	41	115	41	34

Figure S37. Get High-res Image Gene #13: 'Amp Peak 13(7q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 13(7q31.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.03e-09 (Chi-square test), Q value = 7.5e-07

Table S38. Gene #13: 'Amp Peak 13(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 13(7Q31.2) MUTATED	62	12	21	26	26
AMP PEAK 13(7Q31.2) WILD-TYPE	36	63	33	55	18

Figure S38. Get High-res Image Gene #13: 'Amp Peak 13(7q31.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 13(7q31.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.03e-07 (Fisher's exact test), Q value = 7e-05

Table S39. Gene #13: 'Amp Peak 13(7q31.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
AMP PEAK 13(7Q31.2) MUTATED	48	36	63
AMP PEAK 13(7Q31.2) WILD-TYPE	104	69	32

Figure S39. Get High-res Image Gene #13: 'Amp Peak 13(7q31.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 7.62e-10 (Fisher's exact test), Q value = 5.6e-07

Table S40. 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	122	157	70	54
AMP PEAK 14(8P11.21) MUTATED	27	31	30	35
AMP PEAK 14(8P11.21) WILD-TYPE	95	126	40	19

Figure S40. 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 'MRNASEQ_CNMF'

P value = 9.9e-06 (Chi-square test), Q value = 0.0058

Table S41. 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	26	12	20	42	9
AMP PEAK 14(8P11.21) WILD-TYPE	72	63	34	39	35

Figure S41. 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 = 1.26e-07 (Fisher's exact test), Q value = 8.5e-05

Table S42. 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	30	55	24
AMP PEAK 14(8P11.21) WILD-TYPE	122	50	71

Figure S42. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.32e-11 (Fisher's exact test), Q value = 9.9e-09

Table S43. 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	122	157	70	54
AMP PEAK 15(8Q11.1) MUTATED	64	39	38	41
AMP PEAK 15(8Q11.1) WILD-TYPE	58	118	32	13

Figure S43. 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 = 2.16e-05 (Fisher's exact test), Q value = 0.012

Table S44. Gene #15: 'Amp Peak 15(8q11.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 15(8Q11.1) MUTATED	23	69	44
AMP PEAK 15(8Q11.1) WILD-TYPE	55	43	68

Figure S44. 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 = 0.0026

Table S45. 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 S45. 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 S46. 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 S46. 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 = 0.00022

Table S47. 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 S47. 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 = 0.003

Table S48. 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 S48. 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 = 3.49e-13 (Fisher's exact test), Q value = 2.6e-10

Table S49. 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	122	157	70	54
AMP PEAK 16(8Q24.21) MUTATED	84	64	54	49
AMP PEAK 16(8Q24.21) WILD-TYPE	38	93	16	5

Figure S49. 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 = 7.75e-08 (Fisher's exact test), Q value = 5.3e-05

Table S50. Gene #16: 'Amp Peak 16(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 16(8Q24.21) MUTATED	32	90	63
AMP PEAK 16(8Q24.21) WILD-TYPE	46	22	49

Figure S50. 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 = 6.41e-07 (Chi-square test), Q value = 0.00042

Table S51. 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	71	34	27	67	22
AMP PEAK 16(8Q24.21) WILD-TYPE	27	41	27	14	22

Figure S51. 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 = 9.15e-05 (Fisher's exact test), Q value = 0.05

Table S52. 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	68
AMP PEAK 16(8Q24.21) WILD-TYPE	76	28	27

Figure S52. 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 = 6.21e-07 (Fisher's exact test), Q value = 0.00041

Table S53. 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	75	138	35
AMP PEAK 16(8Q24.21) WILD-TYPE	83	45	22

Figure S53. 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 = 6.85e-07 (Fisher's exact test), Q value = 0.00045

Table S54. 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	77	79	92
AMP PEAK 16(8Q24.21) WILD-TYPE	86	36	28

Figure S54. 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 = 9.73e-07 (Fisher's exact test), Q value = 0.00063

Table S55. 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	122	157	70	54
AMP PEAK 17(10P15.1) MUTATED	27	26	27	28
AMP PEAK 17(10P15.1) WILD-TYPE	95	131	43	26

Figure S55. 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 = 2.39e-07 (Fisher's exact test), Q value = 0.00016

Table S56. Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 17(10P15.1) MUTATED	4	41	35
AMP PEAK 17(10P15.1) WILD-TYPE	74	71	77

Figure S56. 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 S57. 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 S57. 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 = 0.0014

Table S58. 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 S58. 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 = 0.095

Table S59. 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 S59. 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 = 2.2e-13 (Fisher's exact test), Q value = 1.7e-10

Table S60. 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	122	157	70	54
AMP PEAK 18(11Q13.3) MUTATED	55	19	33	30
AMP PEAK 18(11Q13.3) WILD-TYPE	67	138	37	24

Figure S60. 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 = 7.27e-06 (Fisher's exact test), Q value = 0.0043

Table S61. Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 18(11Q13.3) MUTATED	14	57	34
AMP PEAK 18(11Q13.3) WILD-TYPE	64	55	78

Figure S61. 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 = 0.018

Table S62. 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 S62. 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 = 0.00024

Table S63. 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 S63. 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 = 3.3e-05

Table S64. 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 S64. 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 = 5.9e-05

Table S65. 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 S65. 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 = 1.72e-17 (Fisher's exact test), Q value = 1.3e-14

Table S66. 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	122	157	70	54
AMP PEAK 19(12P12.1) MUTATED	35	34	57	14
AMP PEAK 19(12P12.1) WILD-TYPE	87	123	13	40

Figure S66. 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 = 1.78e-07 (Fisher's exact test), Q value = 0.00012

Table S67. Gene #19: 'Amp Peak 19(12p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 19(12P12.1) MUTATED	8	44	51
AMP PEAK 19(12P12.1) WILD-TYPE	70	68	61

Figure S67. 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 = 0.00063

Table S68. 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 S68. 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 = 0.0024

Table S69. 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 S69. 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 = 0.0061

Table S70. 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 S70. 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 = 0.0044

Table S71. 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 S71. 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 = 7.88e-18 (Fisher's exact test), Q value = 6e-15

Table S72. 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	122	157	70	54
AMP PEAK 20(12Q14.1) MUTATED	23	31	54	17
AMP PEAK 20(12Q14.1) WILD-TYPE	99	126	16	37

Figure S72. 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 = 1.06e-05 (Fisher's exact test), Q value = 0.0062

Table S73. Gene #20: 'Amp Peak 20(12q14.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 20(12Q14.1) MUTATED	8	40	44
AMP PEAK 20(12Q14.1) WILD-TYPE	70	72	68

Figure S73. 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 = 0.00018

Table S74. 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 S74. 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 = 1.6e-06

Table S75. 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 S75. 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 = 1.8e-05

Table S76. 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 S76. 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 = 7e-06

Table S77. 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 S77. 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 = 6.32e-15 (Fisher's exact test), Q value = 4.8e-12

Table S78. Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 21(12Q15) MUTATED	27	32	52	18
AMP PEAK 21(12Q15) WILD-TYPE	95	125	18	36

Figure S78. 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 = 2.77e-06 (Fisher's exact test), Q value = 0.0017

Table S79. Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 21(12Q15) MUTATED	8	45	43
AMP PEAK 21(12Q15) WILD-TYPE	70	67	69

Figure S79. 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 = 0.00032

Table S80. 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 S80. 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 S81. 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 S81. 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 = 0.00013

Table S82. 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 S82. 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 = 2.9e-06

Table S83. 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 S83. 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 = 2.05e-10 (Fisher's exact test), Q value = 1.5e-07

Table S84. 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	122	157	70	54
AMP PEAK 23(14Q13.3) MUTATED	64	41	34	41
AMP PEAK 23(14Q13.3) WILD-TYPE	58	116	36	13

Figure S84. 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 = 1.28e-05 (Fisher's exact test), Q value = 0.0074

Table S85. Gene #23: 'Amp Peak 23(14q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 23(14Q13.3) MUTATED	28	69	36
AMP PEAK 23(14Q13.3) WILD-TYPE	50	43	76

Figure S85. 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 = 1.9e-07

Table S86. 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 S86. 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 = 0.029

Table S87. 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 S87. 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 S88. 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 S88. 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 = 2.6e-06

Table S89. 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 S89. 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 = 2.67e-12 (Fisher's exact test), Q value = 2e-09

Table S90. Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 24(17Q12) MUTATED	77	35	41	27
AMP PEAK 24(17Q12) WILD-TYPE	45	122	29	27

Figure S90. 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 = 8.86e-07 (Fisher's exact test), Q value = 0.00058

Table S91. Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 24(17Q12) MUTATED	17	67	47
AMP PEAK 24(17Q12) WILD-TYPE	61	45	65

Figure S91. 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 = 6.42e-05 (Fisher's exact test), Q value = 0.036

Table S92. 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	73	83	56
AMP PEAK 24(17Q12) MUTATED	3	38	49	18
AMP PEAK 24(17Q12) WILD-TYPE	20	35	34	38

Figure S92. 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 = 0.00068

Table S93. 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 S93. 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 = 4.6e-05

Table S94. 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 S94. 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 = 0.002

Table S95. 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 S95. 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 = 6.9e-05

Table S96. 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 S96. 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 = 3.34e-13 (Fisher's exact test), Q value = 2.5e-10

Table S97. 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	122	157	70	54
AMP PEAK 25(17Q23.1) MUTATED	85	41	44	25
AMP PEAK 25(17Q23.1) WILD-TYPE	37	116	26	29

Figure S97. 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 = 4.55e-06 (Fisher's exact test), Q value = 0.0028

Table S98. Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
AMP PEAK 25(17Q23.1) MUTATED	18	65	56
AMP PEAK 25(17Q23.1) WILD-TYPE	60	47	56

Figure S98. 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 = 8.12e-08 (Fisher's exact test), Q value = 5.6e-05

Table S99. 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	73	83	56
AMP PEAK 25(17Q23.1) MUTATED	3	43	54	15
AMP PEAK 25(17Q23.1) WILD-TYPE	20	30	29	41

Figure S99. 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 = 0.00012

Table S100. 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 S100. 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 = 2.1e-07

Table S101. 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 S101. 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 = 0.0098

Table S102. 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 S102. 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 = 0.0033

Table S103. 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 S103. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 26(18p11.32) mutation analysis' versus 'CN_CNMF'

P value = 5.64e-08 (Fisher's exact test), Q value = 3.9e-05

Table S104. Gene #26: 'Amp Peak 26(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 26(18P11.32) MUTATED	38	18	20	27
AMP PEAK 26(18P11.32) WILD-TYPE	84	139	50	27

Figure S104. Get High-res Image Gene #26: 'Amp Peak 26(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 26(18p11.32) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.5e-06 (Fisher's exact test), Q value = 0.0045

Table S105. Gene #26: 'Amp Peak 26(18p11.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
AMP PEAK 26(18P11.32) MUTATED	23	32	47
AMP PEAK 26(18P11.32) WILD-TYPE	140	83	73

Figure S105. Get High-res Image Gene #26: 'Amp Peak 26(18p11.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 27(18q11.2) mutation analysis' versus 'CN_CNMF'

P value = 7.99e-06 (Fisher's exact test), Q value = 0.0047

Table S106. Gene #27: 'Amp Peak 27(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 27(18Q11.2) MUTATED	26	19	17	25
AMP PEAK 27(18Q11.2) WILD-TYPE	96	138	53	29

Figure S106. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 27(18q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.45e-06 (Fisher's exact test), Q value = 0.00092

Table S107. Gene #27: 'Amp Peak 27(18q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
AMP PEAK 27(18Q11.2) MUTATED	19	22	45
AMP PEAK 27(18Q11.2) WILD-TYPE	144	93	75

Figure S107. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(19q12) mutation analysis' versus 'CN_CNMF'

P value = 3.41e-07 (Fisher's exact test), Q value = 0.00023

Table S108. Gene #28: 'Amp Peak 28(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 28(19Q12) MUTATED	31	23	32	24
AMP PEAK 28(19Q12) WILD-TYPE	91	134	38	30

Figure S108. Get High-res Image Gene #28: 'Amp Peak 28(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 28(19q12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S109. Gene #28: 'Amp Peak 28(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
AMP PEAK 28(19Q12) MUTATED	24	42	30
AMP PEAK 28(19Q12) WILD-TYPE	128	63	65

Figure S109. Get High-res Image Gene #28: 'Amp Peak 28(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 28(19q12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.36e-06 (Fisher's exact test), Q value = 0.00087

Table S110. Gene #28: 'Amp Peak 28(19q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
AMP PEAK 28(19Q12) MUTATED	23	72	15
AMP PEAK 28(19Q12) WILD-TYPE	135	111	42

Figure S110. Get High-res Image Gene #28: 'Amp Peak 28(19q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 28(19q12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.18e-07 (Fisher's exact test), Q value = 0.00034

Table S111. Gene #28: 'Amp Peak 28(19q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
AMP PEAK 28(19Q12) MUTATED	23	37	50
AMP PEAK 28(19Q12) WILD-TYPE	140	78	70

Figure S111. Get High-res Image Gene #28: 'Amp Peak 28(19q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 29(20q11.21) mutation analysis' versus 'CN_CNMF'

P value = 4.67e-10 (Fisher's exact test), Q value = 3.4e-07

Table S112. Gene #29: 'Amp Peak 29(20q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 29(20Q11.21) MUTATED	62	39	45	34
AMP PEAK 29(20Q11.21) WILD-TYPE	60	118	25	20

Figure S112. Get High-res Image Gene #29: 'Amp Peak 29(20q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 29(20q11.21) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.72e-06 (Fisher's exact test), Q value = 0.004

Table S113. Gene #29: 'Amp Peak 29(20q11.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
AMP PEAK 29(20Q11.21) MUTATED	47	102	27
AMP PEAK 29(20Q11.21) WILD-TYPE	111	81	30

Figure S113. Get High-res Image Gene #29: 'Amp Peak 29(20q11.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 29(20q11.21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.38e-05 (Fisher's exact test), Q value = 0.036

Table S114. Gene #29: 'Amp Peak 29(20q11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
AMP PEAK 29(20Q11.21) MUTATED	51	59	66
AMP PEAK 29(20Q11.21) WILD-TYPE	112	56	54

Figure S114. Get High-res Image Gene #29: 'Amp Peak 29(20q11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 30(20q13.33) mutation analysis' versus 'CN_CNMF'

P value = 4.75e-09 (Fisher's exact test), Q value = 3.4e-06

Table S115. Gene #30: 'Amp Peak 30(20q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 30(20Q13.33) MUTATED	67	47	41	40
AMP PEAK 30(20Q13.33) WILD-TYPE	55	110	29	14

Figure S115. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 30(20q13.33) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.15e-05 (Chi-square test), Q value = 0.0067

Table S116. Gene #30: 'Amp Peak 30(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 30(20Q13.33) MUTATED	50	26	18	58	22
AMP PEAK 30(20Q13.33) WILD-TYPE	48	49	36	23	22

Figure S116. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 30(20q13.33) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.006

Table S117. Gene #30: 'Amp Peak 30(20q13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

Figure S117. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 30(20q13.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.34e-05 (Fisher's exact test), Q value = 0.0077

Table S118. Gene #30: 'Amp Peak 30(20q13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
AMP PEAK 30(20Q13.33) MUTATED	56	61	74
AMP PEAK 30(20Q13.33) WILD-TYPE	107	54	46

Figure S118. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 32(Xq28) mutation analysis' versus 'CN_CNMF'

P value = 2.57e-12 (Fisher's exact test), Q value = 1.9e-09

Table S119. Gene #32: 'Amp Peak 32(Xq28) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
AMP PEAK 32(XQ28) MUTATED	59	18	29	24
AMP PEAK 32(XQ28) WILD-TYPE	63	139	41	30

Figure S119. Get High-res Image Gene #32: 'Amp Peak 32(Xq28) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 32(Xq28) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000272 (Chi-square test), Q value = 0.14

Table S120. Gene #32: 'Amp Peak 32(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 32(XQ28) MUTATED	49	15	12	29	14
AMP PEAK 32(XQ28) WILD-TYPE	49	60	42	52	30

Figure S120. Get High-res Image Gene #32: 'Amp Peak 32(Xq28) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 5.69e-07 (Fisher's exact test), Q value = 0.00037

Table S121. Gene #33: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 1(1P36.13) MUTATED	12	32	24	24
DEL PEAK 1(1P36.13) WILD-TYPE	110	125	46	30

Figure S121. Get High-res Image Gene #33: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 5.33e-05 (Chi-square test), Q value = 0.03

Table S122. Gene #33: '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 S122. Get High-res Image Gene #33: '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 = 0.096

Table S123. Gene #33: '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 S123. Get High-res Image Gene #33: '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 = 0.11

Table S124. Gene #33: '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 S124. Get High-res Image Gene #33: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 4.47e-05 (Fisher's exact test), Q value = 0.025

Table S125. Gene #34: 'Del Peak 2(1p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 2(1P13.1) MUTATED	26	36	33	24
DEL PEAK 2(1P13.1) WILD-TYPE	96	121	37	30

Figure S125. Get High-res Image Gene #34: 'Del Peak 2(1p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 5(3p26.3) mutation analysis' versus 'CN_CNMF'

P value = 7.07e-06 (Fisher's exact test), Q value = 0.0042

Table S126. Gene #37: 'Del Peak 5(3p26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 5(3P26.3) MUTATED	60	48	41	34
DEL PEAK 5(3P26.3) WILD-TYPE	62	109	29	20

Figure S126. Get High-res Image Gene #37: 'Del Peak 5(3p26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 5(3p26.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.14e-06 (Fisher's exact test), Q value = 0.002

Table S127. Gene #37: 'Del Peak 5(3p26.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 5(3P26.3) MUTATED	49	67	45
DEL PEAK 5(3P26.3) WILD-TYPE	103	38	50

Figure S127. Get High-res Image Gene #37: 'Del Peak 5(3p26.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(3p26.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.087

Table S128. Gene #37: 'Del Peak 5(3p26.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 5(3P26.3) MUTATED	51	99	29
DEL PEAK 5(3P26.3) WILD-TYPE	107	84	28

Figure S128. Get High-res Image Gene #37: 'Del Peak 5(3p26.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 5(3p26.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.54e-06 (Fisher's exact test), Q value = 0.0033

Table S129. Gene #37: 'Del Peak 5(3p26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 5(3P26.3) MUTATED	51	56	72
DEL PEAK 5(3P26.3) WILD-TYPE	112	59	48

Figure S129. Get High-res Image Gene #37: 'Del Peak 5(3p26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 9.12e-07 (Fisher's exact test), Q value = 0.00059

Table S130. Gene #38: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 6(3P21.31) MUTATED	62	51	46	35
DEL PEAK 6(3P21.31) WILD-TYPE	60	106	24	19

Figure S130. Get High-res Image Gene #38: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.35e-09 (Fisher's exact test), Q value = 2.4e-06

Table S131. Gene #38: '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 S131. Get High-res Image Gene #38: '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 = 0.005

Table S132. Gene #38: '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 S132. Get High-res Image Gene #38: '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 S133. Gene #38: '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 S133. Get High-res Image Gene #38: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 8.83e-05 (Chi-square test), Q value = 0.049

Table S134. Gene #40: '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 S134. Get High-res Image Gene #40: 'Del Peak 8(3q29) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 9(4p15.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.058

Table S135. Gene #41: 'Del Peak 9(4p15.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
DEL PEAK 9(4P15.2) MUTATED	5	31	32
DEL PEAK 9(4P15.2) WILD-TYPE	73	81	80

Figure S135. Get High-res Image Gene #41: 'Del Peak 9(4p15.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 9(4p15.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.73e-06 (Chi-square test), Q value = 0.0035

Table S136. Gene #41: 'Del Peak 9(4p15.2) 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 9(4P15.2) MUTATED	16	7	16	34	7
DEL PEAK 9(4P15.2) WILD-TYPE	82	68	38	47	37

Figure S136. Get High-res Image Gene #41: 'Del Peak 9(4p15.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 9(4p15.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.99e-07 (Fisher's exact test), Q value = 0.00026

Table S137. Gene #41: 'Del Peak 9(4p15.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 9(4P15.2) MUTATED	18	43	19
DEL PEAK 9(4P15.2) WILD-TYPE	134	62	76

Figure S137. Get High-res Image Gene #41: 'Del Peak 9(4p15.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(4p15.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.18e-06 (Fisher's exact test), Q value = 0.0014

Table S138. Gene #41: 'Del Peak 9(4p15.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 9(4P15.2) MUTATED	18	63	13
DEL PEAK 9(4P15.2) WILD-TYPE	140	120	44

Figure S138. Get High-res Image Gene #41: 'Del Peak 9(4p15.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 9(4p15.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00084

Table S139. Gene #41: 'Del Peak 9(4p15.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 9(4P15.2) MUTATED	19	30	45
DEL PEAK 9(4P15.2) WILD-TYPE	144	85	75

Figure S139. Get High-res Image Gene #41: 'Del Peak 9(4p15.2) 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 = 0.11

Table S140. Gene #42: '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 S140. Get High-res Image Gene #42: '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 = 0.054

Table S141. Gene #42: '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 S141. Get High-res Image Gene #42: '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 = 2.34e-06 (Fisher's exact test), Q value = 0.0015

Table S142. Gene #42: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 10(4Q22.1) MUTATED	33	28	35	23
DEL PEAK 10(4Q22.1) WILD-TYPE	89	129	35	31

Figure S142. Get High-res Image Gene #42: '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 = 0.000345 (Fisher's exact test), Q value = 0.18

Table S143. Gene #42: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
DEL PEAK 10(4Q22.1) MUTATED	10	43	34
DEL PEAK 10(4Q22.1) WILD-TYPE	68	69	78

Figure S143. Get High-res Image Gene #42: '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 = 0.00036

Table S144. Gene #42: '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 S144. Get High-res Image Gene #42: '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 = 2.6e-09

Table S145. Gene #42: '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 S145. Get High-res Image Gene #42: '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 = 0.00034

Table S146. Gene #42: '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 S146. Get High-res Image Gene #42: '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 = 8.1e-06

Table S147. Gene #42: '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 S147. Get High-res Image Gene #42: '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 = 2.47e-09 (Fisher's exact test), Q value = 1.8e-06

Table S148. Gene #43: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 11(4Q35.1) MUTATED	40	32	43	28
DEL PEAK 11(4Q35.1) WILD-TYPE	82	125	27	26

Figure S148. Get High-res Image Gene #43: '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 = 1.61e-08 (Fisher's exact test), Q value = 1.1e-05

Table S149. Gene #43: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
DEL PEAK 11(4Q35.1) MUTATED	8	54	48
DEL PEAK 11(4Q35.1) WILD-TYPE	70	58	64

Figure S149. Get High-res Image Gene #43: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 11(4q35.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.07e-11 (Chi-square test), Q value = 1.5e-08

Table S150. Gene #43: '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 S150. Get High-res Image Gene #43: '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 = 5.9e-14

Table S151. Gene #43: '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 S151. Get High-res Image Gene #43: '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 = 7.6e-06

Table S152. Gene #43: '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 S152. Get High-res Image Gene #43: '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 S153. Gene #43: '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 S153. Get High-res Image Gene #43: '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 = 1.74e-11 (Fisher's exact test), Q value = 1.3e-08

Table S154. Gene #44: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 12(5Q11.2) MUTATED	55	24	38	28
DEL PEAK 12(5Q11.2) WILD-TYPE	67	133	32	26

Figure S154. Get High-res Image Gene #44: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(5q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.01e-05 (Chi-square test), Q value = 0.0059

Table S155. Gene #44: '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 S155. Get High-res Image Gene #44: '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 = 5.4e-05

Table S156. Gene #44: '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 S156. Get High-res Image Gene #44: '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 = 3e-04

Table S157. Gene #44: '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 S157. Get High-res Image Gene #44: '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 = 5.1e-05

Table S158. Gene #44: '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 S158. Get High-res Image Gene #44: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(5q34) mutation analysis' versus 'CN_CNMF'

P value = 5.72e-13 (Fisher's exact test), Q value = 4.3e-10

Table S159. Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 13(5Q34) MUTATED	46	23	43	28
DEL PEAK 13(5Q34) WILD-TYPE	76	134	27	26

Figure S159. Get High-res Image Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(5q34) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.05e-08 (Fisher's exact test), Q value = 1.4e-05

Table S160. Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
DEL PEAK 13(5Q34) MUTATED	8	56	41
DEL PEAK 13(5Q34) WILD-TYPE	70	56	71

Figure S160. Get High-res Image Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 13(5q34) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000302 (Fisher's exact test), Q value = 0.16

Table S161. Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	73	83	56
DEL PEAK 13(5Q34) MUTATED	4	37	31	10
DEL PEAK 13(5Q34) WILD-TYPE	19	36	52	46

Figure S161. Get High-res Image Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 13(5q34) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.81e-07 (Chi-square test), Q value = 0.00063

Table S162. Gene #45: 'Del Peak 13(5q34) 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(5Q34) MUTATED	42	8	17	41	11
DEL PEAK 13(5Q34) WILD-TYPE	56	67	37	40	33

Figure S162. Get High-res Image Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 13(5q34) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.33e-11 (Fisher's exact test), Q value = 6.2e-08

Table S163. Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 13(5Q34) MUTATED	24	58	37
DEL PEAK 13(5Q34) WILD-TYPE	128	47	58

Figure S163. Get High-res Image Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(5q34) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.38e-10 (Fisher's exact test), Q value = 1e-07

Table S164. Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 13(5Q34) MUTATED	28	94	15
DEL PEAK 13(5Q34) WILD-TYPE	130	89	42

Figure S164. Get High-res Image Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 13(5q34) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.78e-10 (Fisher's exact test), Q value = 2.8e-07

Table S165. Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 13(5Q34) MUTATED	27	48	62
DEL PEAK 13(5Q34) WILD-TYPE	136	67	58

Figure S165. Get High-res Image Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(6q22.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.13

Table S166. Gene #47: 'Del Peak 15(6q22.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
DEL PEAK 15(6Q22.31) MUTATED	45	70	41
DEL PEAK 15(6Q22.31) WILD-TYPE	33	42	71

Figure S166. Get High-res Image Gene #47: 'Del Peak 15(6q22.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 17(8p23.2) mutation analysis' versus 'CN_CNMF'

P value = 3.89e-17 (Fisher's exact test), Q value = 3e-14

Table S167. Gene #49: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 17(8P23.2) MUTATED	91	37	42	27
DEL PEAK 17(8P23.2) WILD-TYPE	31	120	28	27

Figure S167. Get High-res Image Gene #49: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 17(8p23.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.05e-05 (Chi-square test), Q value = 0.0062

Table S168. Gene #49: '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 S168. Get High-res Image Gene #49: '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 = 0.00012

Table S169. Gene #49: '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 S169. Get High-res Image Gene #49: '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 S170. Gene #49: '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 S170. Get High-res Image Gene #49: 'Del Peak 17(8p23.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(8p21.3) mutation analysis' versus 'CN_CNMF'

P value = 2.24e-17 (Fisher's exact test), Q value = 1.7e-14

Table S171. Gene #50: 'Del Peak 18(8p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 18(8P21.3) MUTATED	94	41	45	30
DEL PEAK 18(8P21.3) WILD-TYPE	28	116	25	24

Figure S171. Get High-res Image Gene #50: 'Del Peak 18(8p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 18(8p21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.06e-06 (Chi-square test), Q value = 0.0031

Table S172. Gene #50: 'Del Peak 18(8p21.3) 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 18(8P21.3) MUTATED	71	26	21	46	22
DEL PEAK 18(8P21.3) WILD-TYPE	27	49	33	35	22

Figure S172. Get High-res Image Gene #50: 'Del Peak 18(8p21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 18(8p21.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-07 (Fisher's exact test), Q value = 0.00013

Table S173. Gene #50: 'Del Peak 18(8p21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 18(8P21.3) MUTATED	59	56	71
DEL PEAK 18(8P21.3) WILD-TYPE	93	49	24

Figure S173. Get High-res Image Gene #50: 'Del Peak 18(8p21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(8p21.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000303 (Fisher's exact test), Q value = 0.16

Table S174. Gene #50: 'Del Peak 18(8p21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 18(8P21.3) MUTATED	64	114	29
DEL PEAK 18(8P21.3) WILD-TYPE	94	69	28

Figure S174. Get High-res Image Gene #50: 'Del Peak 18(8p21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 18(8p21.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.16e-07 (Fisher's exact test), Q value = 0.00059

Table S175. Gene #50: 'Del Peak 18(8p21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 18(8P21.3) MUTATED	61	79	67
DEL PEAK 18(8P21.3) WILD-TYPE	102	36	53

Figure S175. Get High-res Image Gene #50: 'Del Peak 18(8p21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000157 (Fisher's exact test), Q value = 0.085

Table S176. Gene #51: 'Del Peak 19(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 19(9P23) MUTATED	72	74	54	26
DEL PEAK 19(9P23) WILD-TYPE	50	83	16	28

Figure S176. Get High-res Image Gene #51: 'Del Peak 19(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.89e-05 (Fisher's exact test), Q value = 0.016

Table S177. Gene #52: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 20(9P21.3) MUTATED	74	78	56	24
DEL PEAK 20(9P21.3) WILD-TYPE	48	79	14	30

Figure S177. Get High-res Image Gene #52: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0061

Table S178. Gene #53: 'Del Peak 21(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 21(9Q21.11) MUTATED	61	58	49	34
DEL PEAK 21(9Q21.11) WILD-TYPE	61	99	21	20

Figure S178. Get High-res Image Gene #53: 'Del Peak 21(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 9.41e-06 (Fisher's exact test), Q value = 0.0056

Table S179. Gene #53: 'Del Peak 21(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 21(9Q21.11) MUTATED	59	72	43
DEL PEAK 21(9Q21.11) WILD-TYPE	93	33	52

Figure S179. Get High-res Image Gene #53: 'Del Peak 21(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.2e-05 (Fisher's exact test), Q value = 0.007

Table S180. Gene #53: 'Del Peak 21(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 21(9Q21.11) MUTATED	60	61	78
DEL PEAK 21(9Q21.11) WILD-TYPE	103	54	42

Figure S180. Get High-res Image Gene #53: 'Del Peak 21(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 22(10p15.3) mutation analysis' versus 'CN_CNMF'

P value = 2.69e-06 (Fisher's exact test), Q value = 0.0017

Table S181. Gene #54: 'Del Peak 22(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 22(10P15.3) MUTATED	46	19	23	11
DEL PEAK 22(10P15.3) WILD-TYPE	76	138	47	43

Figure S181. Get High-res Image Gene #54: 'Del Peak 22(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 23(10q26.3) mutation analysis' versus 'CN_CNMF'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0066

Table S182. Gene #55: 'Del Peak 23(10q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 23(10Q26.3) MUTATED	52	25	18	18
DEL PEAK 23(10Q26.3) WILD-TYPE	70	132	52	36

Figure S182. Get High-res Image Gene #55: 'Del Peak 23(10q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 24(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.069

Table S183. Gene #56: 'Del Peak 24(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 24(11P15.5) MUTATED	39	24	29	15
DEL PEAK 24(11P15.5) WILD-TYPE	83	133	41	39

Figure S183. Get High-res Image Gene #56: 'Del Peak 24(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 24(11p15.5) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.98e-06 (Fisher's exact test), Q value = 0.003

Table S184. Gene #56: 'Del Peak 24(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 24(11P15.5) MUTATED	22	44	27
DEL PEAK 24(11P15.5) WILD-TYPE	130	61	68

Figure S184. Get High-res Image Gene #56: 'Del Peak 24(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(11q25) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000464 (Chi-square test), Q value = 0.24

Table S185. Gene #57: 'Del Peak 25(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 25(11Q25) MUTATED	15	11	21	26	6
DEL PEAK 25(11Q25) WILD-TYPE	83	64	33	55	38

Figure S185. Get High-res Image Gene #57: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 28(12q24.33) mutation analysis' versus 'CN_CNMF'

P value = 8.61e-05 (Fisher's exact test), Q value = 0.048

Table S186. Gene #60: 'Del Peak 28(12q24.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 28(12Q24.33) MUTATED	44	37	9	5
DEL PEAK 28(12Q24.33) WILD-TYPE	78	120	61	49

Figure S186. Get High-res Image Gene #60: 'Del Peak 28(12q24.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 28(12q24.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.84e-06 (Fisher's exact test), Q value = 0.0035

Table S187. Gene #60: 'Del Peak 28(12q24.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 28(12Q24.33) MUTATED	54	28	11
DEL PEAK 28(12Q24.33) WILD-TYPE	109	87	109

Figure S187. Get High-res Image Gene #60: 'Del Peak 28(12q24.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.92e-16 (Fisher's exact test), Q value = 1.5e-13

Table S188. Gene #61: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 29(13Q12.11) MUTATED	96	47	47	35
DEL PEAK 29(13Q12.11) WILD-TYPE	26	110	23	19

Figure S188. Get High-res Image Gene #61: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.86e-06 (Fisher's exact test), Q value = 0.0024

Table S189. Gene #61: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	73	83	56
DEL PEAK 29(13Q12.11) MUTATED	8	46	60	18
DEL PEAK 29(13Q12.11) WILD-TYPE	15	27	23	38

Figure S189. Get High-res Image Gene #61: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 2.36e-06 (Chi-square test), Q value = 0.0015

Table S190. Gene #61: 'Del Peak 29(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 29(13Q12.11) MUTATED	66	27	25	59	19
DEL PEAK 29(13Q12.11) WILD-TYPE	32	48	29	22	25

Figure S190. Get High-res Image Gene #61: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3.99e-09 (Fisher's exact test), Q value = 2.9e-06

Table S191. Gene #61: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 29(13Q12.11) MUTATED	56	74	66
DEL PEAK 29(13Q12.11) WILD-TYPE	96	31	29

Figure S191. Get High-res Image Gene #61: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 7.35e-06 (Fisher's exact test), Q value = 0.0044

Table S192. Gene #61: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 29(13Q12.11) MUTATED	66	124	34
DEL PEAK 29(13Q12.11) WILD-TYPE	92	59	23

Figure S192. Get High-res Image Gene #61: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 8.66e-07 (Fisher's exact test), Q value = 0.00056

Table S193. Gene #61: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 29(13Q12.11) MUTATED	66	77	81
DEL PEAK 29(13Q12.11) WILD-TYPE	97	38	39

Figure S193. Get High-res Image Gene #61: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(13q12.13) mutation analysis' versus 'CN_CNMF'

P value = 3.49e-18 (Fisher's exact test), Q value = 2.7e-15

Table S194. Gene #62: 'Del Peak 30(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 30(13Q12.13) MUTATED	98	45	45	36
DEL PEAK 30(13Q12.13) WILD-TYPE	24	112	25	18

Figure S194. Get High-res Image Gene #62: 'Del Peak 30(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 30(13q12.13) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.92e-06 (Fisher's exact test), Q value = 0.0012

Table S195. Gene #62: 'Del Peak 30(13q12.13) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	73	83	56
DEL PEAK 30(13Q12.13) MUTATED	8	46	61	18
DEL PEAK 30(13Q12.13) WILD-TYPE	15	27	22	38

Figure S195. Get High-res Image Gene #62: 'Del Peak 30(13q12.13) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 30(13q12.13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.8e-06 (Chi-square test), Q value = 0.0029

Table S196. Gene #62: 'Del Peak 30(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 30(13Q12.13) MUTATED	66	28	25	59	19
DEL PEAK 30(13Q12.13) WILD-TYPE	32	47	29	22	25

Figure S196. Get High-res Image Gene #62: 'Del Peak 30(13q12.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 30(13q12.13) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.61e-09 (Fisher's exact test), Q value = 6.1e-06

Table S197. Gene #62: 'Del Peak 30(13q12.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 30(13Q12.13) MUTATED	57	73	67
DEL PEAK 30(13Q12.13) WILD-TYPE	95	32	28

Figure S197. Get High-res Image Gene #62: 'Del Peak 30(13q12.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(13q12.13) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.21e-05 (Fisher's exact test), Q value = 0.018

Table S198. Gene #62: 'Del Peak 30(13q12.13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 30(13Q12.13) MUTATED	67	122	34
DEL PEAK 30(13Q12.13) WILD-TYPE	91	61	23

Figure S198. Get High-res Image Gene #62: 'Del Peak 30(13q12.13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 30(13q12.13) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.52e-06 (Fisher's exact test), Q value = 0.0022

Table S199. Gene #62: 'Del Peak 30(13q12.13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 30(13Q12.13) MUTATED	67	75	81
DEL PEAK 30(13Q12.13) WILD-TYPE	96	40	39

Figure S199. Get High-res Image Gene #62: 'Del Peak 30(13q12.13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(13q34) mutation analysis' versus 'CN_CNMF'

P value = 4.14e-10 (Fisher's exact test), Q value = 3e-07

Table S200. Gene #63: 'Del Peak 31(13q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 31(13Q34) MUTATED	74	39	37	33
DEL PEAK 31(13Q34) WILD-TYPE	48	118	33	21

Figure S200. Get High-res Image Gene #63: 'Del Peak 31(13q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 31(13q34) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000366 (Fisher's exact test), Q value = 0.19

Table S201. Gene #63: 'Del Peak 31(13q34) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	73	83	56
DEL PEAK 31(13Q34) MUTATED	7	42	41	13
DEL PEAK 31(13Q34) WILD-TYPE	16	31	42	43

Figure S201. Get High-res Image Gene #63: 'Del Peak 31(13q34) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 31(13q34) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.88e-05 (Chi-square test), Q value = 0.022

Table S202. Gene #63: 'Del Peak 31(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 31(13Q34) MUTATED	52	21	18	51	17
DEL PEAK 31(13Q34) WILD-TYPE	46	54	36	30	27

Figure S202. Get High-res Image Gene #63: 'Del Peak 31(13q34) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 31(13q34) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.1e-06 (Fisher's exact test), Q value = 0.0031

Table S203. Gene #63: 'Del Peak 31(13q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 31(13Q34) MUTATED	46	59	54
DEL PEAK 31(13Q34) WILD-TYPE	106	46	41

Figure S203. Get High-res Image Gene #63: 'Del Peak 31(13q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(13q34) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.13

Table S204. Gene #63: 'Del Peak 31(13q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 31(13Q34) MUTATED	54	63	63
DEL PEAK 31(13Q34) WILD-TYPE	109	52	57

Figure S204. Get High-res Image Gene #63: 'Del Peak 31(13q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(15q11.2) mutation analysis' versus 'CN_CNMF'

P value = 3.27e-11 (Fisher's exact test), Q value = 2.4e-08

Table S205. Gene #65: 'Del Peak 33(15q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 33(15Q11.2) MUTATED	85	46	34	35
DEL PEAK 33(15Q11.2) WILD-TYPE	37	111	36	19

Figure S205. Get High-res Image Gene #65: 'Del Peak 33(15q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 33(15q11.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.095

Table S206. Gene #65: 'Del Peak 33(15q11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	73	83	56
DEL PEAK 33(15Q11.2) MUTATED	10	38	55	16
DEL PEAK 33(15Q11.2) WILD-TYPE	13	35	28	40

Figure S206. Get High-res Image Gene #65: 'Del Peak 33(15q11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 33(15q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.83e-09 (Chi-square test), Q value = 1.3e-06

Table S207. Gene #65: 'Del Peak 33(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 33(15Q11.2) MUTATED	69	27	11	51	21
DEL PEAK 33(15Q11.2) WILD-TYPE	29	48	43	30	23

Figure S207. Get High-res Image Gene #65: 'Del Peak 33(15q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 33(15q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-07 (Fisher's exact test), Q value = 7.2e-05

Table S208. Gene #65: 'Del Peak 33(15q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 33(15Q11.2) MUTATED	59	49	71
DEL PEAK 33(15Q11.2) WILD-TYPE	93	56	24

Figure S208. Get High-res Image Gene #65: 'Del Peak 33(15q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(15q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000156 (Fisher's exact test), Q value = 0.085

Table S209. Gene #65: 'Del Peak 33(15q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 33(15Q11.2) MUTATED	61	70	67
DEL PEAK 33(15Q11.2) WILD-TYPE	102	45	53

Figure S209. Get High-res Image Gene #65: 'Del Peak 33(15q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(15q15.3) mutation analysis' versus 'CN_CNMF'

P value = 1.47e-12 (Fisher's exact test), Q value = 1.1e-09

Table S210. Gene #66: 'Del Peak 34(15q15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 34(15Q15.3) MUTATED	86	45	37	37
DEL PEAK 34(15Q15.3) WILD-TYPE	36	112	33	17

Figure S210. Get High-res Image Gene #66: 'Del Peak 34(15q15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 34(15q15.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 3.26e-06 (Fisher's exact test), Q value = 0.002

Table S211. Gene #66: 'Del Peak 34(15q15.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	73	83	56
DEL PEAK 34(15Q15.3) MUTATED	8	41	59	16
DEL PEAK 34(15Q15.3) WILD-TYPE	15	32	24	40

Figure S211. Get High-res Image Gene #66: 'Del Peak 34(15q15.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 34(15q15.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.87e-10 (Chi-square test), Q value = 6.4e-07

Table S212. Gene #66: 'Del Peak 34(15q15.3) 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 34(15Q15.3) MUTATED	71	27	12	52	23
DEL PEAK 34(15Q15.3) WILD-TYPE	27	48	42	29	21

Figure S212. Get High-res Image Gene #66: 'Del Peak 34(15q15.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 34(15q15.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.32e-08 (Fisher's exact test), Q value = 4.4e-05

Table S213. Gene #66: 'Del Peak 34(15q15.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 34(15Q15.3) MUTATED	59	54	72
DEL PEAK 34(15Q15.3) WILD-TYPE	93	51	23

Figure S213. Get High-res Image Gene #66: 'Del Peak 34(15q15.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(15q15.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.059

Table S214. Gene #66: 'Del Peak 34(15q15.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 34(15Q15.3) MUTATED	61	113	29
DEL PEAK 34(15Q15.3) WILD-TYPE	97	70	28

Figure S214. Get High-res Image Gene #66: 'Del Peak 34(15q15.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 34(15q15.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.31e-07 (Fisher's exact test), Q value = 0.00035

Table S215. Gene #66: 'Del Peak 34(15q15.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 34(15Q15.3) MUTATED	57	73	73
DEL PEAK 34(15Q15.3) WILD-TYPE	106	42	47

Figure S215. Get High-res Image Gene #66: 'Del Peak 34(15q15.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.33e-05 (Fisher's exact test), Q value = 0.013

Table S216. Gene #67: 'Del Peak 35(16q23.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 35(16Q23.3) MUTATED	54	34	31	26
DEL PEAK 35(16Q23.3) WILD-TYPE	68	123	39	28

Figure S216. Get High-res Image Gene #67: 'Del Peak 35(16q23.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 5.06e-06 (Chi-square test), Q value = 0.0031

Table S217. Gene #67: 'Del Peak 35(16q23.3) 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 35(16Q23.3) MUTATED	49	15	14	40	9
DEL PEAK 35(16Q23.3) WILD-TYPE	49	60	40	41	35

Figure S217. Get High-res Image Gene #67: 'Del Peak 35(16q23.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 2.77e-06 (Fisher's exact test), Q value = 0.0017

Table S218. Gene #67: 'Del Peak 35(16q23.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 35(16Q23.3) MUTATED	33	46	48
DEL PEAK 35(16Q23.3) WILD-TYPE	119	59	47

Figure S218. Get High-res Image Gene #67: 'Del Peak 35(16q23.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(17p13.3) mutation analysis' versus 'CN_CNMF'

P value = 1.11e-11 (Fisher's exact test), Q value = 8.3e-09

Table S219. Gene #68: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 36(17P13.3) MUTATED	92	53	46	32
DEL PEAK 36(17P13.3) WILD-TYPE	30	104	24	22

Figure S219. Get High-res Image Gene #68: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 36(17p13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.83e-05 (Chi-square test), Q value = 0.038

Table S220. Gene #68: 'Del Peak 36(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 36(17P13.3) MUTATED	72	29	28	52	22
DEL PEAK 36(17P13.3) WILD-TYPE	26	46	26	29	22

Figure S220. Get High-res Image Gene #68: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 36(17p13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.38e-06 (Fisher's exact test), Q value = 0.0038

Table S221. Gene #68: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 36(17P13.3) MUTATED	67	65	71
DEL PEAK 36(17P13.3) WILD-TYPE	85	40	24

Figure S221. Get High-res Image Gene #68: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(18q21.32) mutation analysis' versus 'CN_CNMF'

P value = 8.39e-09 (Fisher's exact test), Q value = 6e-06

Table S222. Gene #69: 'Del Peak 37(18q21.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 37(18Q21.32) MUTATED	84	56	43	18
DEL PEAK 37(18Q21.32) WILD-TYPE	38	101	27	36

Figure S222. Get High-res Image Gene #69: 'Del Peak 37(18q21.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.2e-09 (Fisher's exact test), Q value = 8.7e-07

Table S223. Gene #70: 'Del Peak 38(18q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 38(18Q23) MUTATED	84	52	42	18
DEL PEAK 38(18Q23) WILD-TYPE	38	105	28	36

Figure S223. Get High-res Image Gene #70: 'Del Peak 38(18q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.00038 (Chi-square test), Q value = 0.2

Table S224. Gene #70: 'Del Peak 38(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 38(18Q23) MUTATED	65	28	26	31	25
DEL PEAK 38(18Q23) WILD-TYPE	33	47	28	50	19

Figure S224. Get High-res Image Gene #70: 'Del Peak 38(18q23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 4.38e-10 (Fisher's exact test), Q value = 3.2e-07

Table S225. Gene #71: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 39(19P13.3) MUTATED	65	58	58	35
DEL PEAK 39(19P13.3) WILD-TYPE	57	99	12	19

Figure S225. Get High-res Image Gene #71: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.15e-06 (Chi-square test), Q value = 0.0014

Table S226. Gene #71: 'Del Peak 39(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 39(19P13.3) MUTATED	49	34	34	63	14
DEL PEAK 39(19P13.3) WILD-TYPE	49	41	20	18	30

Figure S226. Get High-res Image Gene #71: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 1.9e-08 (Fisher's exact test), Q value = 1.3e-05

Table S227. Gene #71: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 39(19P13.3) MUTATED	61	81	52
DEL PEAK 39(19P13.3) WILD-TYPE	91	24	43

Figure S227. Get High-res Image Gene #71: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0015

Table S228. Gene #71: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 39(19P13.3) MUTATED	67	122	22
DEL PEAK 39(19P13.3) WILD-TYPE	91	61	35

Figure S228. Get High-res Image Gene #71: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 9.36e-06 (Fisher's exact test), Q value = 0.0055

Table S229. Gene #71: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 39(19P13.3) MUTATED	66	62	83
DEL PEAK 39(19P13.3) WILD-TYPE	97	53	37

Figure S229. Get High-res Image Gene #71: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 40(19p13.2) mutation analysis' versus 'CN_CNMF'

P value = 7.84e-10 (Fisher's exact test), Q value = 5.7e-07

Table S230. Gene #72: 'Del Peak 40(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 40(19P13.2) MUTATED	62	54	55	36
DEL PEAK 40(19P13.2) WILD-TYPE	60	103	15	18

Figure S230. Get High-res Image Gene #72: 'Del Peak 40(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 40(19p13.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.06e-06 (Chi-square test), Q value = 0.00068

Table S231. Gene #72: 'Del Peak 40(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 40(19P13.2) MUTATED	49	32	29	63	13
DEL PEAK 40(19P13.2) WILD-TYPE	49	43	25	18	31

Figure S231. Get High-res Image Gene #72: 'Del Peak 40(19p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 40(19p13.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.00082

Table S232. Gene #72: 'Del Peak 40(19p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 40(19P13.2) MUTATED	59	75	52
DEL PEAK 40(19P13.2) WILD-TYPE	93	30	43

Figure S232. Get High-res Image Gene #72: 'Del Peak 40(19p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(19p13.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.00094

Table S233. Gene #72: 'Del Peak 40(19p13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 40(19P13.2) MUTATED	65	118	19
DEL PEAK 40(19P13.2) WILD-TYPE	93	65	38

Figure S233. Get High-res Image Gene #72: 'Del Peak 40(19p13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 40(19p13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.99e-07 (Fisher's exact test), Q value = 0.00033

Table S234. Gene #72: 'Del Peak 40(19p13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 40(19P13.2) MUTATED	62	56	84
DEL PEAK 40(19P13.2) WILD-TYPE	101	59	36

Figure S234. Get High-res Image Gene #72: 'Del Peak 40(19p13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 41(19q11) mutation analysis' versus 'CN_CNMF'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.0097

Table S235. Gene #73: 'Del Peak 41(19q11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 41(19Q11) MUTATED	51	25	24	14
DEL PEAK 41(19Q11) WILD-TYPE	71	132	46	40

Figure S235. Get High-res Image Gene #73: 'Del Peak 41(19q11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 41(19q11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000213 (Fisher's exact test), Q value = 0.11

Table S236. Gene #73: 'Del Peak 41(19q11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 41(19Q11) MUTATED	27	36	38
DEL PEAK 41(19Q11) WILD-TYPE	125	69	57

Figure S236. Get High-res Image Gene #73: 'Del Peak 41(19q11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(19q13.33) mutation analysis' versus 'CN_CNMF'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00072

Table S237. Gene #74: 'Del Peak 42(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 42(19Q13.33) MUTATED	59	32	31	25
DEL PEAK 42(19Q13.33) WILD-TYPE	63	125	39	29

Figure S237. Get High-res Image Gene #74: 'Del Peak 42(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 42(19q13.33) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000137 (Fisher's exact test), Q value = 0.074

Table S238. Gene #74: 'Del Peak 42(19q13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 42(19Q13.33) MUTATED	38	84	21
DEL PEAK 42(19Q13.33) WILD-TYPE	120	99	36

Figure S238. Get High-res Image Gene #74: 'Del Peak 42(19q13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 42(19q13.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0068

Table S239. Gene #74: 'Del Peak 42(19q13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 42(19Q13.33) MUTATED	37	48	58
DEL PEAK 42(19Q13.33) WILD-TYPE	126	67	62

Figure S239. Get High-res Image Gene #74: 'Del Peak 42(19q13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 43(21q11.2) mutation analysis' versus 'CN_CNMF'

P value = 4.23e-08 (Fisher's exact test), Q value = 3e-05

Table S240. Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 43(21Q11.2) MUTATED	27	44	43	26
DEL PEAK 43(21Q11.2) WILD-TYPE	95	113	27	28

Figure S240. Get High-res Image Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 43(21q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.11e-05 (Fisher's exact test), Q value = 0.018

Table S241. Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
DEL PEAK 43(21Q11.2) MUTATED	12	52	40
DEL PEAK 43(21Q11.2) WILD-TYPE	66	60	72

Figure S241. Get High-res Image Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 43(21q11.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 7.72e-05 (Fisher's exact test), Q value = 0.043

Table S242. Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	73	83	56
DEL PEAK 43(21Q11.2) MUTATED	5	42	21	16
DEL PEAK 43(21Q11.2) WILD-TYPE	18	31	62	40

Figure S242. Get High-res Image Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 43(21q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.83e-08 (Chi-square test), Q value = 6e-05

Table S243. Gene #75: 'Del Peak 43(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 43(21Q11.2) MUTATED	33	9	24	46	11
DEL PEAK 43(21Q11.2) WILD-TYPE	65	66	30	35	33

Figure S243. Get High-res Image Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 43(21q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.62e-09 (Fisher's exact test), Q value = 3.3e-06

Table S244. Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 43(21Q11.2) MUTATED	30	60	33
DEL PEAK 43(21Q11.2) WILD-TYPE	122	45	62

Figure S244. Get High-res Image Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 43(21q11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.011

Table S245. Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 43(21Q11.2) MUTATED	35	84	18
DEL PEAK 43(21Q11.2) WILD-TYPE	123	99	39

Figure S245. Get High-res Image Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 43(21q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.83e-06 (Fisher's exact test), Q value = 0.0035

Table S246. Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 43(21Q11.2) MUTATED	37	39	61
DEL PEAK 43(21Q11.2) WILD-TYPE	126	76	59

Figure S246. Get High-res Image Gene #75: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 44(22q13.32) mutation analysis' versus 'CN_CNMF'

P value = 1.3e-12 (Fisher's exact test), Q value = 9.8e-10

Table S247. Gene #76: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 44(22Q13.32) MUTATED	65	42	45	42
DEL PEAK 44(22Q13.32) WILD-TYPE	57	115	25	12

Figure S247. Get High-res Image Gene #76: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 44(22q13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.77e-08 (Fisher's exact test), Q value = 4.7e-05

Table S248. Gene #76: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	112	112
DEL PEAK 44(22Q13.32) MUTATED	19	74	52
DEL PEAK 44(22Q13.32) WILD-TYPE	59	38	60

Figure S248. Get High-res Image Gene #76: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 44(22q13.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.08e-09 (Chi-square test), Q value = 3.6e-06

Table S249. Gene #76: 'Del Peak 44(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 44(22Q13.32) MUTATED	55	22	26	58	9
DEL PEAK 44(22Q13.32) WILD-TYPE	43	53	28	23	35

Figure S249. Get High-res Image Gene #76: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 44(22q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.88e-09 (Fisher's exact test), Q value = 3.5e-06

Table S250. Gene #76: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	105	95
DEL PEAK 44(22Q13.32) MUTATED	46	71	53
DEL PEAK 44(22Q13.32) WILD-TYPE	106	34	42

Figure S250. Get High-res Image Gene #76: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 44(22q13.32) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.67e-05 (Fisher's exact test), Q value = 0.0096

Table S251. Gene #76: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	183	57
DEL PEAK 44(22Q13.32) MUTATED	58	111	22
DEL PEAK 44(22Q13.32) WILD-TYPE	100	72	35

Figure S251. Get High-res Image Gene #76: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 44(22q13.32) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.76e-08 (Fisher's exact test), Q value = 2.6e-05

Table S252. Gene #76: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	115	120
DEL PEAK 44(22Q13.32) MUTATED	51	62	78
DEL PEAK 44(22Q13.32) WILD-TYPE	112	53	42

Figure S252. Get High-res Image Gene #76: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 45(Xp22.2) mutation analysis' versus 'CN_CNMF'

P value = 3.83e-07 (Fisher's exact test), Q value = 0.00025

Table S253. Gene #77: 'Del Peak 45(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	157	70	54
DEL PEAK 45(XP22.2) MUTATED	53	22	24	18
DEL PEAK 45(XP22.2) WILD-TYPE	69	135	46	36

Figure S253. Get High-res Image Gene #77: 'Del Peak 45(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 = 403
Number of copy number variation regions = 77
Number of molecular subtypes = 10
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

[4] GISTIC_version2

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