Correlation between copy number variation genes and molecular subtypes

Overview

Introduction

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

Summary

Testing the association between copy number variation of 63 peak regions and 10 molecular subtypes across 891 patients, 442 significant findings detected with Q value < 0.25.

Amp Peak 1(1p22.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 2(1q21.3) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 3(1q44) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 4(3p26.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 5(3q26.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 6(4q13.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 7(6p23) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 8(6q21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 9(8p11.23) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 10(8p11.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 11(8q24.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 12(10p15.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 13(10q22.3) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 14(11p13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 15(11q13.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 16(11q14.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 17(12p13.33) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 18(12q15) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Amp Peak 19(13q12.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Amp Peak 20(13q34) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 21(14q21.1) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 22(15q26.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 23(17p11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 24(17q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 25(17q23.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Amp Peak 26(19q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 27(19q13.42) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 28(20q13.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 1(1p36.13) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Del Peak 2(1p21.2) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 3(2q37.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 4(3p14.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 5(4p16.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 6(4q35.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 7(5q11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 8(5q21.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 9(6p25.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 10(6q15) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 11(6q27) cnvs correlated to 'CN_CNMF'.
Del Peak 12(7p22.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 13(7q36.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 14(8p23.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 15(8p11.21) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 16(9p21.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 17(9q21.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 18(10q23.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 19(10q26.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 20(11p15.5) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 21(11q23.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 22(12p13.1) cnvs correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 23(12q24.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 24(13q14.2) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 25(14q24.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 26(15q13.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 27(16q24.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 28(17p12) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 29(17q21.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 30(18q23) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 31(19p13.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 32(19q13.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 33(20p13) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 34(21q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 35(22q13.32) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 63 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 442 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	Chi-square test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 1(1p22 3)	203 (23%)	688	1.49e-06 (0.000475)	6.58e-12 (2.99e-09)	3.43e-16 (1.8e-13)	7.13e-14 (3.49e-11)	0.000151 (0.0345)	1.74e-07 (6.06e-05)	2.3e-15 (1.18e-12)	8.7e-17 (4.64e-14)	2.72e-14 (1.34e-11)	3.24e-18 (1.78e-15)
Amp Peak 5(3q26 32)	286 (32%)	605	4.54e-11 (2.02e-08)	1.51e-10 (6.48e-08)	2.58e-37 (1.58e-34)	3.92e-15 (1.98e-12)	1.21e-06 (0.000389)	5.9e-06 (0.0017)	1.95e-23 (1.13e-20)	1.71e-20 (9.68e-18)	2.8e-16 (1.48e-13)	6.24e-21 (3.55e-18)
Amp Peak 7(6p23)	235 (26%)	656	5.85e-11 (2.57e-08)	6.05e-09 (2.36e-06)	8.38e-33 (5.07e-30)	2.58e-15 (1.32e-12)	1e-06 (0.000323)	7.41e-05 (0.0181)	1.87e-14 (9.36e-12)	6.83e-11 (2.99e-08)	9.53e-19 (5.27e-16)	2.91e-16 (1.54e-13)
Amp Peak 8(6q21)	165 (19%)	726	2.8e-15 (1.43e-12)	6.15e-10 (2.55e-07)	1.01e-39 (6.21e-37)	1.09e-11 (4.95e-09)	1.04e-08 (3.95e-06)	4.91e-07 (0.000162)	6.64e-24 (3.87e-21)	2.22e-18 (1.22e-15)	3.13e-21 (1.78e-18)	2.86e-26 (1.69e-23)
Amp Peak 11(8q24 21)	573 (64%)	318	3.61e-10 (1.52e-07)	2.03e-10 (8.62e-08)	1.77e-45 (1.1e-42)	5.57e-23 (3.22e-20)	3.68e-08 (1.34e-05)	5.27e-07 (0.000174)	2.34e-20 (1.31e-17)	6.88e-13 (3.27e-10)	3.18e-24 (1.86e-21)	1.55e-19 (8.65e-17)
Amp Peak 12(10p15 1)	253 (28%)	638	7.97e-17 (4.26e-14)	4.18e-19 (2.32e-16)	4.58e-35 (2.79e-32)	9.02e-24 (5.24e-21)	1.43e-10 (6.14e-08)	1.46e-12 (6.88e-10)	2.52e-29 (1.51e-26)	3.1e-28 (1.85e-25)	1.73e-27 (1.03e-24)	6.45e-35 (3.93e-32)
Amp Peak 17(12p13 33)	232 (26%)	659	1.74e-10 (7.43e-08)	1.35e-13 (6.57e-11)	3.32e-28 (1.98e-25)	4.4e-15 (2.22e-12)	6.79e-08 (2.42e-05)	3.08e-07 (0.000104)	1.79e-17 (9.7e-15)	2.09e-15 (1.08e-12)	4.16e-22 (2.39e-19)	3.45e-19 (1.92e-16)
Amp Peak 20(13q34)	157 (18%)	734	0.0011 (0.211)	8.57e-10 (3.53e-07)	1.9e-20 (1.07e-17)	2.37e-12 (1.1e-09)	4.1e-06 (0.0012)	2.88e-08 (1.06e-05)	3.54e-16 (1.86e-13)	3.05e-15 (1.55e-12)	2.36e-15 (1.21e-12)	1.26e-19 (7.04e-17)
Amp Peak 26(19q12)	231 (26%)	660	5.61e-08 (2.03e-05)	5.55e-12 (2.53e-09)	1.81e-24 (1.06e-21)	1.37e-08 (5.21e-06)	6.56e-07 (0.000216)	1.51e-06 (0.000478)	3.87e-14 (1.91e-11)	4.67e-17 (2.51e-14)	2.36e-12 (1.1e-09)	1.69e-17 (9.15e-15)
Del Peak 3(2q37 3)	263 (30%)	628	7.69e-07 (0.00025)	5.89e-09 (2.3e-06)	5.27e-20 (2.96e-17)	4.74e-10 (1.97e-07)	1.32e-08 (5e-06)	1.53e-07 (5.33e-05)	3.19e-11 (1.42e-08)	2.2e-07 (7.55e-05)	3.3e-12 (1.52e-09)	2.58e-07 (8.82e-05)
Del Peak 4(3p14 3)	274 (31%)	617	2.23e-13 (1.08e-10)	8.42e-09 (3.25e-06)	2.26e-32 (1.37e-29)	4.65e-12 (2.13e-09)	2.21e-09 (8.82e-07)	1.2e-05 (0.00336)	1.63e-16 (8.67e-14)	5.37e-11 (2.37e-08)	9.81e-20 (5.49e-17)	2.27e-14 (1.13e-11)
Del Peak 5(4p16 3)	279 (31%)	612	1.39e-10 (5.97e-08)	3.16e-12 (1.47e-09)	2.46e-27 (1.46e-24)	8.82e-12 (4.01e-09)	6.65e-07 (0.000218)	3.22e-06 (0.000969)	2.72e-22 (1.57e-19)	5.6e-18 (3.06e-15)	1.12e-14 (5.6e-12)	3.71e-15 (1.88e-12)
Del Peak 6(4q35 2)	280 (31%)	611	7.12e-10 (2.94e-07)	1.92e-07 (6.65e-05)	7.04e-36 (4.3e-33)	5.96e-14 (2.92e-11)	3.47e-08 (1.27e-05)	2.09e-06 (0.000651)	3.04e-21 (1.73e-18)	1.18e-15 (6.12e-13)	1e-15 (5.23e-13)	2.34e-17 (1.26e-14)
Del Peak 7(5q11 2)	231 (26%)	660	8.07e-22 (4.63e-19)	5.58e-26 (3.28e-23)	3.42e-62 (2.15e-59)	3.27e-36 (2e-33)	1.99e-15 (1.02e-12)	1.27e-18 (7.04e-16)	3.1e-41 (1.92e-38)	8.36e-44 (5.19e-41)	6.02e-41 (3.72e-38)	2.35e-49 (1.47e-46)
Del Peak 8(5q21 3)	223 (25%)	668	5.18e-25 (3.03e-22)	1.83e-27 (1.09e-24)	2.4e-74 (1.51e-71)	1.41e-50 (8.82e-48)	5.76e-15 (2.9e-12)	2.82e-15 (1.44e-12)	2.89e-48 (1.8e-45)	5.1e-49 (3.18e-46)	2.74e-40 (1.69e-37)	2.29e-53 (1.44e-50)
Del Peak 18(10q23 31)	258 (29%)	633	4.65e-07 (0.000155)	9.23e-05 (0.0221)	1.31e-18 (7.21e-16)	5.14e-11 (2.27e-08)	5.69e-08 (2.05e-05)	2.15e-05 (0.00578)	2.38e-12 (1.11e-09)	6.39e-08 (2.29e-05)	4.41e-09 (1.73e-06)	4.12e-09 (1.63e-06)
Del Peak 19(10q26 3)	259 (29%)	632	1.75e-09 (7e-07)	3.68e-07 (0.000124)	1.02e-19 (5.69e-17)	1.24e-10 (5.38e-08)	2.12e-08 (7.97e-06)	1.92e-07 (6.65e-05)	1.56e-15 (8.08e-13)	2.26e-10 (9.58e-08)	1.66e-13 (8.04e-11)	1.91e-12 (8.96e-10)
Del Peak 20(11p15 5)	259 (29%)	632	5.04e-11 (2.23e-08)	6.22e-08 (2.24e-05)	3e-30 (1.8e-27)	1.01e-09 (4.12e-07)	2.51e-09 (9.98e-07)	3.81e-06 (0.00114)	1.05e-16 (5.57e-14)	3.64e-12 (1.68e-09)	7.33e-17 (3.92e-14)	7.13e-17 (3.82e-14)
Del Peak 23(12q24 31)	162 (18%)	729	1.7e-10 (7.3e-08)	9.29e-11 (4.05e-08)	1.9e-19 (1.06e-16)	2.87e-13 (1.38e-10)	1.44e-05 (0.00399)	7.16e-07 (0.000234)	6.91e-17 (3.71e-14)	2.16e-16 (1.14e-13)	3.28e-12 (1.52e-09)	3.24e-12 (1.5e-09)
Del Peak 25(14q24 3)	286 (32%)	605	2.58e-07 (8.82e-05)	1.05e-09 (4.29e-07)	6.75e-33 (4.09e-30)	4.58e-13 (2.19e-10)	2.51e-07 (8.62e-05)	2.89e-06 (0.00088)	1.99e-14 (9.91e-12)	1.1e-12 (5.22e-10)	8.25e-18 (4.51e-15)	1.23e-20 (6.98e-18)
Del Peak 26(15q13 1)	310 (35%)	581	2.12e-06 (0.000657)	3.26e-08 (1.2e-05)	9.29e-31 (5.6e-28)	5.25e-12 (2.4e-09)	0.000316 (0.0683)	4.78e-05 (0.012)	3.27e-15 (1.66e-12)	1.43e-12 (6.74e-10)	1.02e-15 (5.32e-13)	2.67e-21 (1.53e-18)
Del Peak 27(16q24 3)	575 (65%)	316	1.76e-12 (8.28e-10)	5.68e-13 (2.7e-10)	6.56e-11 (2.88e-08)	4.16e-10 (1.74e-07)	1.71e-09 (6.89e-07)	2.08e-11 (9.36e-09)	3.34e-18 (1.83e-15)	1.19e-17 (6.49e-15)	5.67e-14 (2.79e-11)	1.99e-20 (1.12e-17)
Del Peak 29(17q21 31)	312 (35%)	579	2.35e-12 (1.1e-09)	3.82e-07 (0.000128)	9.31e-23 (5.37e-20)	4.98e-14 (2.45e-11)	1.55e-11 (7e-09)	5.88e-11 (2.58e-08)	1.21e-20 (6.87e-18)	1.17e-15 (6.1e-13)	1.78e-14 (8.9e-12)	2.77e-16 (1.47e-13)
Del Peak 31(19p13 3)	301 (34%)	590	1.08e-09 (4.39e-07)	9.68e-09 (3.72e-06)	3.97e-43 (2.46e-40)	4.05e-17 (2.18e-14)	2.67e-06 (0.000821)	4.31e-05 (0.011)	3.11e-13 (1.49e-10)	2.3e-09 (9.16e-07)	9.07e-16 (4.73e-13)	2.14e-14 (1.07e-11)
Del Peak 32(19q13 32)	180 (20%)	711	3.03e-05 (0.00806)	8.29e-06 (0.00237)	1.77e-17 (9.6e-15)	3.07e-11 (1.37e-08)	0.000469 (0.0989)	4.52e-05 (0.0114)	4.4e-09 (1.73e-06)	1.39e-06 (0.000444)	1.37e-10 (5.94e-08)	2.46e-08 (9.16e-06)
Amp Peak 22(15q26 3)	162 (18%)	729	3.16e-07 (0.000107)	0.000286 (0.0624)	2.36e-14 (1.17e-11)	0.00091 (0.18)	0.000168 (0.038)	0.0263 (1.00)	5.25e-08 (1.91e-05)	3.29e-05 (0.00865)	1.37e-07 (4.8e-05)	4.18e-10 (1.74e-07)
Del Peak 17(9q21 11)	239 (27%)	652	0.000914 (0.18)	1.98e-05 (0.00536)	9.57e-18 (5.22e-15)	9.77e-10 (4.01e-07)	1.44e-05 (0.00399)	0.00515 (0.788)	2.82e-06 (0.000862)	8.67e-05 (0.0209)	8.68e-09 (3.34e-06)	1.35e-09 (5.45e-07)
Amp Peak 4(3p26 1)	182 (20%)	709	0.000534 (0.11)	3.45e-05 (0.00902)	5.1e-13 (2.43e-10)	3.28e-07 (0.00011)	0.0063 (0.926)	0.00638 (0.931)	5.03e-10 (2.09e-07)	3.45e-05 (0.00902)	1.01e-08 (3.86e-06)	2.95e-06 (0.000894)
Amp Peak 6(4q13 3)	141 (16%)	750	0.00085 (0.17)	0.000555 (0.114)	3.34e-16 (1.76e-13)	8.72e-07 (0.000282)	0.0838 (1.00)	0.562 (1.00)	1.01e-05 (0.00286)	0.000523 (0.109)	0.000649 (0.132)	2.8e-07 (9.52e-05)
Amp Peak 28(20q13 2)	455 (51%)	436	2.58e-08 (9.54e-06)	1.22e-06 (0.000391)	3.23e-49 (2.02e-46)	2.07e-20 (1.16e-17)	0.000494 (0.104)	0.00994 (1.00)	1.17e-09 (4.75e-07)	0.0185 (1.00)	3.02e-11 (1.35e-08)	2.29e-08 (8.58e-06)
Del Peak 12(7p22 3)	117 (13%)	774	0.000233 (0.0513)	0.000547 (0.113)	7.09e-16 (3.71e-13)	1.54e-05 (0.00424)	0.0222 (1.00)	0.00556 (0.834)	7.93e-09 (3.07e-06)	3.72e-06 (0.00111)	3.9e-10 (1.63e-07)	3.62e-09 (1.43e-06)
Del Peak 14(8p23 2)	469 (53%)	422	3.44e-05 (0.00902)	2.92e-06 (0.000886)	1.15e-30 (6.91e-28)	2.92e-10 (1.23e-07)	0.0112 (1.00)	0.03 (1.00)	2.38e-11 (1.07e-08)	2.01e-06 (0.000626)	5.35e-08 (1.94e-05)	1.5e-09 (6.03e-07)
Del Peak 33(20p13)	132 (15%)	759	0.00206 (0.36)	1.42e-05 (0.00396)	9.52e-14 (4.64e-11)	3.97e-07 (0.000133)	0.00085 (0.17)	0.00683 (0.99)	1.8e-10 (7.68e-08)	2.57e-08 (9.53e-06)	1.06e-11 (4.79e-09)	1.74e-09 (7e-07)
Del Peak 16(9p21 3)	298 (33%)	593	1.01e-05 (0.00287)	3.96e-06 (0.00117)	7.63e-29 (4.57e-26)	2.76e-14 (1.36e-11)	0.00342 (0.543)	0.338 (1.00)	1.14e-07 (4.02e-05)	0.00183 (0.323)	9.58e-10 (3.94e-07)	5.19e-05 (0.013)
Del Peak 24(13q14 2)	407 (46%)	484	0.0102 (1.00)	3.07e-05 (0.00814)	2.43e-28 (1.46e-25)	2.51e-06 (0.000773)	0.559 (1.00)	0.104 (1.00)	1.34e-07 (4.69e-05)	3.45e-05 (0.00902)	1.55e-08 (5.87e-06)	2.62e-05 (0.00701)
Amp Peak 2(1q21 3)	645 (72%)	246	0.0199 (1.00)	0.000122 (0.0282)	1.02e-10 (4.46e-08)	0.000194 (0.0435)	0.0717 (1.00)	0.00817 (1.00)	0.000292 (0.0634)	0.00104 (0.2)	3.95e-05 (0.0101)	0.0043 (0.671)
Amp Peak 13(10q22 3)	129 (14%)	762	5.45e-05 (0.0135)	0.0536 (1.00)	1.01e-09 (4.12e-07)	0.000226 (0.0499)	0.00279 (0.458)	0.0146 (1.00)	9.93e-08 (3.51e-05)	0.00171 (0.304)	5.17e-06 (0.00149)	0.000147 (0.0337)
Amp Peak 16(11q14 1)	220 (25%)	671	0.0143 (1.00)	0.0783 (1.00)	4.58e-13 (2.19e-10)	3.14e-05 (0.0083)	0.0703 (1.00)	0.189 (1.00)	0.000112 (0.0261)	0.00121 (0.23)	4.64e-07 (0.000155)	7.01e-05 (0.0172)
Amp Peak 18(12q15)	228 (26%)	663	1.75e-06 (0.000551)	6.29e-08 (2.26e-05)	1.6e-25 (9.36e-23)	1.64e-13 (7.95e-11)	0.187 (1.00)	0.0724 (1.00)	1.17e-05 (0.00331)	0.0105 (1.00)	6.14e-09 (2.39e-06)	0.175 (1.00)
Amp Peak 21(14q21 1)	179 (20%)	712	0.0123 (1.00)	0.00043 (0.0911)	1.03e-13 (5.04e-11)	3.91e-06 (0.00116)	0.127 (1.00)	0.0459 (1.00)	1.65e-05 (0.00453)	0.00123 (0.232)	0.000113 (0.0264)	0.0261 (1.00)
Amp Peak 24(17q12)	289 (32%)	602	0.000108 (0.0256)	1.51e-05 (0.00418)	9.14e-37 (5.6e-34)	8.72e-08 (3.09e-05)	0.0476 (1.00)	0.00547 (0.826)	6.59e-05 (0.0162)	0.0253 (1.00)	0.00163 (0.295)	0.000416 (0.0885)
Amp Peak 25(17q23 1)	367 (41%)	524	0.000367 (0.0788)	5.11e-05 (0.0128)	4.12e-40 (2.54e-37)	4.73e-09 (1.86e-06)	0.189 (1.00)	0.462 (1.00)	0.000199 (0.0443)	0.327 (1.00)	1.72e-06 (0.000541)	0.0445 (1.00)
Del Peak 28(17p12)	537 (60%)	354	4.01e-06 (0.00118)	0.054 (1.00)	1.35e-21 (7.75e-19)	2.15e-07 (7.43e-05)	0.000114 (0.0264)	0.00818 (1.00)	0.00285 (0.461)	0.0986 (1.00)	1.49e-06 (0.000474)	1.81e-06 (0.000567)
Del Peak 30(18q23)	290 (33%)	601	6.04e-06 (0.00173)	0.0272 (1.00)	3.87e-12 (1.78e-09)	1.02e-08 (3.88e-06)	0.00601 (0.896)	0.596 (1.00)	2.74e-05 (0.00731)	0.0396 (1.00)	4.31e-05 (0.011)	0.000169 (0.0381)
Amp Peak 14(11p13)	186 (21%)	705	0.0017 (0.304)	0.112 (1.00)	3.3e-08 (1.21e-05)	0.000751 (0.152)	0.0969 (1.00)	0.14 (1.00)	8.03e-05 (0.0194)	0.0282 (1.00)	3.5e-05 (0.00904)	1.39e-05 (0.00391)
Amp Peak 27(19q13 42)	232 (26%)	659	0.000202 (0.0449)	0.00138 (0.26)	5.8e-15 (2.92e-12)	4.71e-06 (0.00137)	0.00161 (0.294)	0.0495 (1.00)	0.00459 (0.711)	0.0242 (1.00)	1.89e-05 (0.00513)	9.44e-05 (0.0225)
Del Peak 1(1p36 13)	373 (42%)	518	0.00609 (0.901)	3.17e-06 (0.000959)	3e-33 (1.82e-30)	6.69e-08 (2.39e-05)	0.00536 (0.815)	0.0639 (1.00)	4.33e-06 (0.00126)	0.0028 (0.458)	3.4e-11 (1.51e-08)	0.104 (1.00)
Del Peak 10(6q15)	293 (33%)	598	0.0795 (1.00)	0.000985 (0.191)	1.45e-26 (8.57e-24)	1.07e-07 (3.79e-05)	0.396 (1.00)	0.105 (1.00)	1.98e-05 (0.00536)	8e-05 (0.0194)	0.0529 (1.00)	0.00161 (0.294)
Del Peak 13(7q36 1)	173 (19%)	718	0.000562 (0.115)	0.00776 (1.00)	2.34e-08 (8.73e-06)	0.069 (1.00)	0.606 (1.00)	0.0735 (1.00)	0.000824 (0.166)	0.0438 (1.00)	7.75e-09 (3.01e-06)	1.57e-06 (0.000496)
Amp Peak 10(8p11 21)	345 (39%)	546	0.259 (1.00)	0.153 (1.00)	3e-25 (1.76e-22)	3.77e-05 (0.0097)	0.78 (1.00)	0.68 (1.00)	5.22e-05 (0.013)	0.000134 (0.0309)	0.0372 (1.00)	0.207 (1.00)
Del Peak 2(1p21 2)	301 (34%)	590	0.0114 (1.00)	0.000109 (0.0257)	4.04e-23 (2.34e-20)	8.77e-05 (0.021)	0.00164 (0.296)	0.0112 (1.00)	0.000366 (0.0788)	0.00139 (0.261)	0.00221 (0.38)	0.00388 (0.609)
Del Peak 15(8p11 21)	170 (19%)	721	0.000175 (0.0394)	0.00259 (0.433)	1.12e-10 (4.84e-08)	0.019 (1.00)	0.036 (1.00)	0.0184 (1.00)	0.000996 (0.192)	0.0393 (1.00)	0.0213 (1.00)	4.97e-06 (0.00144)
Amp Peak 9(8p11 23)	335 (38%)	556	0.041 (1.00)	0.00826 (1.00)	3.12e-26 (1.84e-23)	2.47e-10 (1.05e-07)	0.0486 (1.00)	0.00925 (1.00)	1.76e-05 (0.0048)	0.00266 (0.438)	0.16 (1.00)	0.0374 (1.00)
Amp Peak 19(13q12 3)	125 (14%)	766	0.00885 (1.00)	0.0282 (1.00)	9.35e-06 (0.00266)	0.0195 (1.00)	0.00907 (1.00)	0.106 (1.00)	2.18e-06 (0.000674)	0.0151 (1.00)	3.53e-06 (0.00106)	0.00505 (0.777)
Amp Peak 3(1q44)	642 (72%)	249	0.387 (1.00)	0.067 (1.00)	2.17e-08 (8.12e-06)	0.000527 (0.11)	0.928 (1.00)	0.345 (1.00)	0.335 (1.00)	0.533 (1.00)	0.417 (1.00)	0.64 (1.00)
Amp Peak 15(11q13 3)	340 (38%)	551	0.231 (1.00)	0.0253 (1.00)	6.2e-34 (3.77e-31)	1.83e-08 (6.89e-06)	0.957 (1.00)	0.174 (1.00)	0.0424 (1.00)	0.32 (1.00)	0.00213 (0.368)	0.119 (1.00)
Del Peak 9(6p25 3)	167 (19%)	724	0.918 (1.00)	0.542 (1.00)	4.07e-06 (0.0012)	5.56e-05 (0.0137)	0.469 (1.00)	0.587 (1.00)	0.00221 (0.38)	0.0616 (1.00)	0.0403 (1.00)	0.103 (1.00)
Del Peak 21(11q23 2)	442 (50%)	449	0.00819 (1.00)	0.0832 (1.00)	3.59e-26 (2.11e-23)	3.17e-10 (1.33e-07)	0.919 (1.00)	0.507 (1.00)	0.00141 (0.263)	0.00262 (0.434)	0.0106 (1.00)	0.00307 (0.49)
Del Peak 22(12p13 1)	156 (18%)	735	0.0316 (1.00)	0.067 (1.00)	0.00226 (0.384)	0.0154 (1.00)	0.244 (1.00)	0.0506 (1.00)	0.00145 (0.269)	0.0173 (1.00)	0.000962 (0.188)	9.45e-05 (0.0225)
Del Peak 34(21q11 2)	181 (20%)	710	0.00209 (0.364)	0.0593 (1.00)	1.38e-12 (6.53e-10)	0.000275 (0.0602)	0.309 (1.00)	0.504 (1.00)	0.0105 (1.00)	0.235 (1.00)	0.0172 (1.00)	0.0735 (1.00)
Amp Peak 23(17p11 2)	124 (14%)	767	0.151 (1.00)	0.0305 (1.00)	7.6e-07 (0.000248)	0.00299 (0.482)	0.358 (1.00)	0.613 (1.00)	0.00236 (0.397)	0.0707 (1.00)	0.183 (1.00)	0.342 (1.00)
Del Peak 11(6q27)	303 (34%)	588	0.148 (1.00)	0.398 (1.00)	3.04e-13 (1.46e-10)	0.00234 (0.396)	0.0524 (1.00)	0.581 (1.00)	0.486 (1.00)	0.52 (1.00)	0.159 (1.00)	0.611 (1.00)
Del Peak 35(22q13 32)	399 (45%)	492	0.0703 (1.00)	0.109 (1.00)	0.000936 (0.183)	0.00146 (0.269)	0.111 (1.00)	0.0188 (1.00)	0.00201 (0.354)	0.0208 (1.00)	0.00342 (0.543)	0.169 (1.00)

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

P value = 1.49e-06 (Fisher's exact test), Q value = 0.00047

Table S1. Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 1(1P22.3) MUTATED	44	12	59
AMP PEAK 1(1P22.3) WILD-TYPE	212	80	100

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 6.58e-12 (Fisher's exact test), Q value = 3e-09

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 1(1P22.3) MUTATED	55	49	11
AMP PEAK 1(1P22.3) WILD-TYPE	66	203	123

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

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

P value = 3.43e-16 (Chi-square test), Q value = 1.8e-13

Table S3. Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 1(1P22.3) MUTATED	45	30	26	86	16
AMP PEAK 1(1P22.3) WILD-TYPE	301	46	172	129	40

Figure S3. Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 7.13e-14 (Chi-square test), Q value = 3.5e-11

Table S4. Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 1(1P22.3) MUTATED	50	23	18	14	2	14
AMP PEAK 1(1P22.3) WILD-TYPE	46	119	62	109	34	76

Figure S4. Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 0.000151 (Fisher's exact test), Q value = 0.035

Table S5. Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
AMP PEAK 1(1P22.3) MUTATED	52	27	16
AMP PEAK 1(1P22.3) WILD-TYPE	94	102	99

Figure S5. Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 1.74e-07 (Fisher's exact test), Q value = 6.1e-05

Table S6. Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
AMP PEAK 1(1P22.3) MUTATED	31	12	52
AMP PEAK 1(1P22.3) WILD-TYPE	125	96	74

Figure S6. Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 2.3e-15 (Fisher's exact test), Q value = 1.2e-12

Table S7. Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 1(1P22.3) MUTATED	96	15	70
AMP PEAK 1(1P22.3) WILD-TYPE	139	140	364

Figure S7. Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 8.7e-17 (Fisher's exact test), Q value = 4.6e-14

Table S8. Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 1(1P22.3) MUTATED	71	23	87
AMP PEAK 1(1P22.3) WILD-TYPE	342	193	108

Figure S8. Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.72e-14 (Fisher's exact test), Q value = 1.3e-11

Table S9. Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 1(1P22.3) MUTATED	32	65	103
AMP PEAK 1(1P22.3) WILD-TYPE	168	358	146

Figure S9. Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 3.24e-18 (Fisher's exact test), Q value = 1.8e-15

Table S10. Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 1(1P22.3) MUTATED	96	93	11
AMP PEAK 1(1P22.3) WILD-TYPE	108	516	48

Figure S10. Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000122 (Fisher's exact test), Q value = 0.028

Table S11. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 2(1Q21.3) MUTATED	103	189	83
AMP PEAK 2(1Q21.3) WILD-TYPE	18	63	51

Figure S11. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.02e-10 (Chi-square test), Q value = 4.5e-08

Table S12. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 2(1Q21.3) MUTATED	213	76	149	166	41
AMP PEAK 2(1Q21.3) WILD-TYPE	133	0	49	49	15

Figure S12. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000194 (Chi-square test), Q value = 0.043

Table S13. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 2(1Q21.3) MUTATED	78	110	65	81	20	53
AMP PEAK 2(1Q21.3) WILD-TYPE	18	32	15	42	16	37

Figure S13. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 0.000292 (Fisher's exact test), Q value = 0.063

Table S14. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 2(1Q21.3) MUTATED	191	99	305
AMP PEAK 2(1Q21.3) WILD-TYPE	44	56	129

Figure S14. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 0.00104 (Fisher's exact test), Q value = 0.2

Table S15. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 2(1Q21.3) MUTATED	297	140	158
AMP PEAK 2(1Q21.3) WILD-TYPE	116	76	37

Figure S15. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.95e-05 (Fisher's exact test), Q value = 0.01

Table S16. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 2(1Q21.3) MUTATED	130	294	205
AMP PEAK 2(1Q21.3) WILD-TYPE	70	129	44

Figure S16. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 3(1q44) mutation analysis' versus 'CN_CNMF'

P value = 2.17e-08 (Chi-square test), Q value = 8.1e-06

Table S17. Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 3(1Q44) MUTATED	224	76	149	157	36
AMP PEAK 3(1Q44) WILD-TYPE	122	0	49	58	20

Figure S17. Get High-res Image Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 3(1q44) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000527 (Chi-square test), Q value = 0.11

Table S18. Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 3(1Q44) MUTATED	69	112	69	77	23	56
AMP PEAK 3(1Q44) WILD-TYPE	27	30	11	46	13	34

Figure S18. Get High-res Image Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 4(3p26.1) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000534 (Fisher's exact test), Q value = 0.11

Table S19. Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 4(3P26.1) MUTATED	49	17	56
AMP PEAK 4(3P26.1) WILD-TYPE	207	75	103

Figure S19. Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 4(3p26.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.45e-05 (Fisher's exact test), Q value = 0.009

Table S20. Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 4(3P26.1) MUTATED	35	73	14
AMP PEAK 4(3P26.1) WILD-TYPE	86	179	120

Figure S20. Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 4(3p26.1) mutation analysis' versus 'CN_CNMF'

P value = 5.1e-13 (Chi-square test), Q value = 2.4e-10

Table S21. Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 4(3P26.1) MUTATED	26	21	50	72	13
AMP PEAK 4(3P26.1) WILD-TYPE	320	55	148	143	43

Figure S21. Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 4(3p26.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.28e-07 (Chi-square test), Q value = 0.00011

Table S22. Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 4(3P26.1) MUTATED	30	7	21	28	3	11
AMP PEAK 4(3P26.1) WILD-TYPE	66	135	59	95	33	79

Figure S22. Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 4(3p26.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.03e-10 (Fisher's exact test), Q value = 2.1e-07

Table S23. Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 4(3P26.1) MUTATED	75	9	88
AMP PEAK 4(3P26.1) WILD-TYPE	160	146	346

Figure S23. Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 4(3p26.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.45e-05 (Fisher's exact test), Q value = 0.009

Table S24. Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 4(3P26.1) MUTATED	90	25	57
AMP PEAK 4(3P26.1) WILD-TYPE	323	191	138

Figure S24. Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 4(3p26.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.01e-08 (Fisher's exact test), Q value = 3.9e-06

Table S25. Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 4(3P26.1) MUTATED	23	69	82
AMP PEAK 4(3P26.1) WILD-TYPE	177	354	167

Figure S25. Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 4(3p26.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.95e-06 (Fisher's exact test), Q value = 0.00089

Table S26. Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 4(3P26.1) MUTATED	64	94	16
AMP PEAK 4(3P26.1) WILD-TYPE	140	515	43

Figure S26. Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 5(3q26.32) mutation analysis' versus 'MRNA_CNMF'

P value = 4.54e-11 (Fisher's exact test), Q value = 2e-08

Table S27. Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 5(3Q26.32) MUTATED	65	23	91
AMP PEAK 5(3Q26.32) WILD-TYPE	191	69	68

Figure S27. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 5(3q26.32) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.51e-10 (Fisher's exact test), Q value = 6.5e-08

Table S28. Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 5(3Q26.32) MUTATED	70	85	24
AMP PEAK 5(3Q26.32) WILD-TYPE	51	167	110

Figure S28. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 5(3q26.32) mutation analysis' versus 'CN_CNMF'

P value = 2.58e-37 (Chi-square test), Q value = 1.6e-34

Table S29. Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 5(3Q26.32) MUTATED	33	27	75	135	16
AMP PEAK 5(3Q26.32) WILD-TYPE	313	49	123	80	40

Figure S29. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 5(3q26.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.92e-15 (Chi-square test), Q value = 2e-12

Table S30. Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 5(3Q26.32) MUTATED	59	16	28	36	9	17
AMP PEAK 5(3Q26.32) WILD-TYPE	37	126	52	87	27	73

Figure S30. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 5(3q26.32) mutation analysis' versus 'RPPA_CNMF'

P value = 1.21e-06 (Fisher's exact test), Q value = 0.00039

Table S31. Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
AMP PEAK 5(3Q26.32) MUTATED	76	35	28
AMP PEAK 5(3Q26.32) WILD-TYPE	70	94	87

Figure S31. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 5(3q26.32) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 5.9e-06 (Fisher's exact test), Q value = 0.0017

Table S32. Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
AMP PEAK 5(3Q26.32) MUTATED	48	25	66
AMP PEAK 5(3Q26.32) WILD-TYPE	108	83	60

Figure S32. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 5(3q26.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.95e-23 (Fisher's exact test), Q value = 1.1e-20

Table S33. Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 5(3Q26.32) MUTATED	137	19	119
AMP PEAK 5(3Q26.32) WILD-TYPE	98	136	315

Figure S33. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 5(3q26.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.71e-20 (Fisher's exact test), Q value = 9.7e-18

Table S34. Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 5(3Q26.32) MUTATED	116	40	119
AMP PEAK 5(3Q26.32) WILD-TYPE	297	176	76

Figure S34. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 5(3q26.32) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.8e-16 (Fisher's exact test), Q value = 1.5e-13

Table S35. Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 5(3Q26.32) MUTATED	45	100	133
AMP PEAK 5(3Q26.32) WILD-TYPE	155	323	116

Figure S35. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 5(3q26.32) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.24e-21 (Fisher's exact test), Q value = 3.6e-18

Table S36. Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 5(3Q26.32) MUTATED	121	136	21
AMP PEAK 5(3Q26.32) WILD-TYPE	83	473	38

Figure S36. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(4q13.3) mutation analysis' versus 'MRNA_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.17

Table S37. Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 6(4Q13.3) MUTATED	34	8	40
AMP PEAK 6(4Q13.3) WILD-TYPE	222	84	119

Figure S37. Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 6(4q13.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000555 (Fisher's exact test), Q value = 0.11

Table S38. Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 6(4Q13.3) MUTATED	28	45	9
AMP PEAK 6(4Q13.3) WILD-TYPE	93	207	125

Figure S38. Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 6(4q13.3) mutation analysis' versus 'CN_CNMF'

P value = 3.34e-16 (Chi-square test), Q value = 1.8e-13

Table S39. Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 6(4Q13.3) MUTATED	19	2	58	54	8
AMP PEAK 6(4Q13.3) WILD-TYPE	327	74	140	161	48

Figure S39. Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 6(4q13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.72e-07 (Chi-square test), Q value = 0.00028

Table S40. Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 6(4Q13.3) MUTATED	25	5	11	30	4	8
AMP PEAK 6(4Q13.3) WILD-TYPE	71	137	69	93	32	82

Figure S40. Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 6(4q13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0029

Table S41. Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 6(4Q13.3) MUTATED	57	10	69
AMP PEAK 6(4Q13.3) WILD-TYPE	178	145	365

Figure S41. Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 6(4q13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000523 (Fisher's exact test), Q value = 0.11

Table S42. Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 6(4Q13.3) MUTATED	60	26	50
AMP PEAK 6(4Q13.3) WILD-TYPE	353	190	145

Figure S42. Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(4q13.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000649 (Fisher's exact test), Q value = 0.13

Table S43. Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 6(4Q13.3) MUTATED	26	54	59
AMP PEAK 6(4Q13.3) WILD-TYPE	174	369	190

Figure S43. Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 6(4q13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.8e-07 (Fisher's exact test), Q value = 9.5e-05

Table S44. Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 6(4Q13.3) MUTATED	57	70	12
AMP PEAK 6(4Q13.3) WILD-TYPE	147	539	47

Figure S44. Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 7(6p23) mutation analysis' versus 'MRNA_CNMF'

P value = 5.85e-11 (Fisher's exact test), Q value = 2.6e-08

Table S45. Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 7(6P23) MUTATED	51	15	78
AMP PEAK 7(6P23) WILD-TYPE	205	77	81

Figure S45. Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 7(6p23) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.05e-09 (Fisher's exact test), Q value = 2.4e-06

Table S46. Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 7(6P23) MUTATED	57	70	17
AMP PEAK 7(6P23) WILD-TYPE	64	182	117

Figure S46. Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 7(6p23) mutation analysis' versus 'CN_CNMF'

P value = 8.38e-33 (Chi-square test), Q value = 5.1e-30

Table S47. Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 7(6P23) MUTATED	23	18	62	116	16
AMP PEAK 7(6P23) WILD-TYPE	323	58	136	99	40

Figure S47. Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 7(6p23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.58e-15 (Chi-square test), Q value = 1.3e-12

Table S48. Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 7(6P23) MUTATED	47	11	20	45	2	11
AMP PEAK 7(6P23) WILD-TYPE	49	131	60	78	34	79

Figure S48. Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 7(6p23) mutation analysis' versus 'RPPA_CNMF'

P value = 1e-06 (Fisher's exact test), Q value = 0.00032

Table S49. Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
AMP PEAK 7(6P23) MUTATED	64	23	23
AMP PEAK 7(6P23) WILD-TYPE	82	106	92

Figure S49. Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 7(6p23) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 7.41e-05 (Fisher's exact test), Q value = 0.018

Table S50. Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
AMP PEAK 7(6P23) MUTATED	32	24	54
AMP PEAK 7(6P23) WILD-TYPE	124	84	72

Figure S50. Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 7(6p23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.87e-14 (Fisher's exact test), Q value = 9.4e-12

Table S51. Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 7(6P23) MUTATED	105	16	100
AMP PEAK 7(6P23) WILD-TYPE	130	139	334

Figure S51. Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 7(6p23) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.83e-11 (Fisher's exact test), Q value = 3e-08

Table S52. Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 7(6P23) MUTATED	96	36	89
AMP PEAK 7(6P23) WILD-TYPE	317	180	106

Figure S52. Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(6p23) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.53e-19 (Fisher's exact test), Q value = 5.3e-16

Table S53. Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 7(6P23) MUTATED	29	76	118
AMP PEAK 7(6P23) WILD-TYPE	171	347	131

Figure S53. Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 7(6p23) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.91e-16 (Fisher's exact test), Q value = 1.5e-13

Table S54. Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 7(6P23) MUTATED	97	106	20
AMP PEAK 7(6P23) WILD-TYPE	107	503	39

Figure S54. Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 8(6q21) mutation analysis' versus 'MRNA_CNMF'

P value = 2.8e-15 (Fisher's exact test), Q value = 1.4e-12

Table S55. Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 8(6Q21) MUTATED	24	12	68
AMP PEAK 8(6Q21) WILD-TYPE	232	80	91

Figure S55. Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 8(6q21) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.15e-10 (Fisher's exact test), Q value = 2.5e-07

Table S56. Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 8(6Q21) MUTATED	50	42	12
AMP PEAK 8(6Q21) WILD-TYPE	71	210	122

Figure S56. Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 8(6q21) mutation analysis' versus 'CN_CNMF'

P value = 1.01e-39 (Chi-square test), Q value = 6.2e-37

Table S57. Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 8(6Q21) MUTATED	21	13	18	107	6
AMP PEAK 8(6Q21) WILD-TYPE	325	63	180	108	50

Figure S57. Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 8(6q21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.09e-11 (Chi-square test), Q value = 4.9e-09

Table S58. Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 8(6Q21) MUTATED	37	3	16	18	2	16
AMP PEAK 8(6Q21) WILD-TYPE	59	139	64	105	34	74

Figure S58. Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 8(6q21) mutation analysis' versus 'RPPA_CNMF'

P value = 1.04e-08 (Fisher's exact test), Q value = 3.9e-06

Table S59. Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
AMP PEAK 8(6Q21) MUTATED	54	12	15
AMP PEAK 8(6Q21) WILD-TYPE	92	117	100

Figure S59. Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 8(6q21) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.91e-07 (Fisher's exact test), Q value = 0.00016

Table S60. Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
AMP PEAK 8(6Q21) MUTATED	20	14	47
AMP PEAK 8(6Q21) WILD-TYPE	136	94	79

Figure S60. Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 8(6q21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.64e-24 (Fisher's exact test), Q value = 3.9e-21

Table S61. Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 8(6Q21) MUTATED	97	7	51
AMP PEAK 8(6Q21) WILD-TYPE	138	148	383

Figure S61. Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 8(6q21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.22e-18 (Fisher's exact test), Q value = 1.2e-15

Table S62. Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 8(6Q21) MUTATED	57	17	81
AMP PEAK 8(6Q21) WILD-TYPE	356	199	114

Figure S62. Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 8(6q21) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.13e-21 (Fisher's exact test), Q value = 1.8e-18

Table S63. Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 8(6Q21) MUTATED	24	36	96
AMP PEAK 8(6Q21) WILD-TYPE	176	387	153

Figure S63. Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 8(6q21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.86e-26 (Fisher's exact test), Q value = 1.7e-23

Table S64. Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 8(6Q21) MUTATED	88	52	16
AMP PEAK 8(6Q21) WILD-TYPE	116	557	43

Figure S64. Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 9(8p11.23) mutation analysis' versus 'CN_CNMF'

P value = 3.12e-26 (Chi-square test), Q value = 1.8e-23

Table S65. Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 9(8P11.23) MUTATED	92	34	95	59	55
AMP PEAK 9(8P11.23) WILD-TYPE	254	42	103	156	1

Figure S65. Get High-res Image Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 9(8p11.23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.47e-10 (Chi-square test), Q value = 1e-07

Table S66. Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 9(8P11.23) MUTATED	31	34	33	79	11	26
AMP PEAK 9(8P11.23) WILD-TYPE	65	108	47	44	25	64

Figure S66. Get High-res Image Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 9(8p11.23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.0048

Table S67. Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 9(8P11.23) MUTATED	76	43	200
AMP PEAK 9(8P11.23) WILD-TYPE	159	112	234

Figure S67. Get High-res Image Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 10(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 3e-25 (Chi-square test), Q value = 1.8e-22

Table S68. Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 10(8P11.21) MUTATED	88	40	81	80	56
AMP PEAK 10(8P11.21) WILD-TYPE	258	36	117	135	0

Figure S68. Get High-res Image Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 10(8p11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.77e-05 (Chi-square test), Q value = 0.0097

Table S69. Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 10(8P11.21) MUTATED	45	35	30	65	10	30
AMP PEAK 10(8P11.21) WILD-TYPE	51	107	50	58	26	60

Figure S69. Get High-res Image Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 10(8p11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.22e-05 (Fisher's exact test), Q value = 0.013

Table S70. Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 10(8P11.21) MUTATED	102	37	184
AMP PEAK 10(8P11.21) WILD-TYPE	133	118	250

Figure S70. Get High-res Image Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 10(8p11.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000134 (Fisher's exact test), Q value = 0.031

Table S71. Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 10(8P11.21) MUTATED	179	59	85
AMP PEAK 10(8P11.21) WILD-TYPE	234	157	110

Figure S71. Get High-res Image Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.61e-10 (Fisher's exact test), Q value = 1.5e-07

Table S72. Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 11(8Q24.21) MUTATED	154	53	139
AMP PEAK 11(8Q24.21) WILD-TYPE	102	39	20

Figure S72. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 2.03e-10 (Fisher's exact test), Q value = 8.6e-08

Table S73. Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 11(8Q24.21) MUTATED	104	178	64
AMP PEAK 11(8Q24.21) WILD-TYPE	17	74	70

Figure S73. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.77e-45 (Chi-square test), Q value = 1.1e-42

Table S74. Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 11(8Q24.21) MUTATED	129	43	152	196	53
AMP PEAK 11(8Q24.21) WILD-TYPE	217	33	46	19	3

Figure S74. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 5.57e-23 (Chi-square test), Q value = 3.2e-20

Table S75. Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 11(8Q24.21) MUTATED	85	42	56	96	16	46
AMP PEAK 11(8Q24.21) WILD-TYPE	11	100	24	27	20	44

Figure S75. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 3.68e-08 (Fisher's exact test), Q value = 1.3e-05

Table S76. Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
AMP PEAK 11(8Q24.21) MUTATED	124	69	74
AMP PEAK 11(8Q24.21) WILD-TYPE	22	60	41

Figure S76. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 5.27e-07 (Fisher's exact test), Q value = 0.00017

Table S77. Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
AMP PEAK 11(8Q24.21) MUTATED	98	61	108
AMP PEAK 11(8Q24.21) WILD-TYPE	58	47	18

Figure S77. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 2.34e-20 (Fisher's exact test), Q value = 1.3e-17

Table S78. Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 11(8Q24.21) MUTATED	200	61	275
AMP PEAK 11(8Q24.21) WILD-TYPE	35	94	159

Figure S78. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 6.88e-13 (Fisher's exact test), Q value = 3.3e-10

Table S79. Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 11(8Q24.21) MUTATED	261	110	165
AMP PEAK 11(8Q24.21) WILD-TYPE	152	106	30

Figure S79. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.18e-24 (Fisher's exact test), Q value = 1.9e-21

Table S80. Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 11(8Q24.21) MUTATED	97	240	221
AMP PEAK 11(8Q24.21) WILD-TYPE	103	183	28

Figure S80. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 1.55e-19 (Fisher's exact test), Q value = 8.7e-17

Table S81. Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 11(8Q24.21) MUTATED	179	333	46
AMP PEAK 11(8Q24.21) WILD-TYPE	25	276	13

Figure S81. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 12(10p15.1) mutation analysis' versus 'MRNA_CNMF'

P value = 7.97e-17 (Fisher's exact test), Q value = 4.3e-14

Table S82. Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 12(10P15.1) MUTATED	43	25	91
AMP PEAK 12(10P15.1) WILD-TYPE	213	67	68

Figure S82. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 12(10p15.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.18e-19 (Fisher's exact test), Q value = 2.3e-16

Table S83. Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 12(10P15.1) MUTATED	79	60	20
AMP PEAK 12(10P15.1) WILD-TYPE	42	192	114

Figure S83. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(10p15.1) mutation analysis' versus 'CN_CNMF'

P value = 4.58e-35 (Chi-square test), Q value = 2.8e-32

Table S84. Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 12(10P15.1) MUTATED	37	20	53	131	12
AMP PEAK 12(10P15.1) WILD-TYPE	309	56	145	84	44

Figure S84. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 12(10p15.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.02e-24 (Chi-square test), Q value = 5.2e-21

Table S85. Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 12(10P15.1) MUTATED	61	5	23	29	2	24
AMP PEAK 12(10P15.1) WILD-TYPE	35	137	57	94	34	66

Figure S85. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 12(10p15.1) mutation analysis' versus 'RPPA_CNMF'

P value = 1.43e-10 (Fisher's exact test), Q value = 6.1e-08

Table S86. Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
AMP PEAK 12(10P15.1) MUTATED	77	21	29
AMP PEAK 12(10P15.1) WILD-TYPE	69	108	86

Figure S86. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 12(10p15.1) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.46e-12 (Fisher's exact test), Q value = 6.9e-10

Table S87. Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
AMP PEAK 12(10P15.1) MUTATED	28	26	73
AMP PEAK 12(10P15.1) WILD-TYPE	128	82	53

Figure S87. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 12(10p15.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.52e-29 (Fisher's exact test), Q value = 1.5e-26

Table S88. Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 12(10P15.1) MUTATED	136	22	78
AMP PEAK 12(10P15.1) WILD-TYPE	99	133	356

Figure S88. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 12(10p15.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.1e-28 (Fisher's exact test), Q value = 1.9e-25

Table S89. Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 12(10P15.1) MUTATED	72	44	120
AMP PEAK 12(10P15.1) WILD-TYPE	341	172	75

Figure S89. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(10p15.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.73e-27 (Fisher's exact test), Q value = 1e-24

Table S90. Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 12(10P15.1) MUTATED	43	64	137
AMP PEAK 12(10P15.1) WILD-TYPE	157	359	112

Figure S90. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 12(10p15.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.45e-35 (Fisher's exact test), Q value = 3.9e-32

Table S91. Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 12(10P15.1) MUTATED	126	95	23
AMP PEAK 12(10P15.1) WILD-TYPE	78	514	36

Figure S91. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 13(10q22.3) mutation analysis' versus 'MRNA_CNMF'

P value = 5.45e-05 (Fisher's exact test), Q value = 0.014

Table S92. Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 13(10Q22.3) MUTATED	25	15	42
AMP PEAK 13(10Q22.3) WILD-TYPE	231	77	117

Figure S92. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 13(10q22.3) mutation analysis' versus 'CN_CNMF'

P value = 1.01e-09 (Chi-square test), Q value = 4.1e-07

Table S93. Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 13(10Q22.3) MUTATED	21	14	28	58	8
AMP PEAK 13(10Q22.3) WILD-TYPE	325	62	170	157	48

Figure S93. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 13(10q22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000226 (Chi-square test), Q value = 0.05

Table S94. Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 13(10Q22.3) MUTATED	23	6	14	19	2	10
AMP PEAK 13(10Q22.3) WILD-TYPE	73	136	66	104	34	80

Figure S94. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 13(10q22.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.93e-08 (Fisher's exact test), Q value = 3.5e-05

Table S95. Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 13(10Q22.3) MUTATED	61	11	50
AMP PEAK 13(10Q22.3) WILD-TYPE	174	144	384

Figure S95. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 13(10q22.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.17e-06 (Fisher's exact test), Q value = 0.0015

Table S96. Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 13(10Q22.3) MUTATED	17	49	59
AMP PEAK 13(10Q22.3) WILD-TYPE	183	374	190

Figure S96. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 13(10q22.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000147 (Fisher's exact test), Q value = 0.034

Table S97. Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 13(10Q22.3) MUTATED	41	68	16
AMP PEAK 13(10Q22.3) WILD-TYPE	163	541	43

Figure S97. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 14(11p13) mutation analysis' versus 'CN_CNMF'

P value = 3.3e-08 (Chi-square test), Q value = 1.2e-05

Table S98. Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 14(11P13) MUTATED	37	15	58	64	12
AMP PEAK 14(11P13) WILD-TYPE	309	61	140	151	44

Figure S98. Get High-res Image Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 14(11p13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000751 (Chi-square test), Q value = 0.15

Table S99. Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 14(11P13) MUTATED	27	18	15	38	3	15
AMP PEAK 14(11P13) WILD-TYPE	69	124	65	85	33	75

Figure S99. Get High-res Image Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 14(11p13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.03e-05 (Fisher's exact test), Q value = 0.019

Table S100. Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 14(11P13) MUTATED	70	18	92
AMP PEAK 14(11P13) WILD-TYPE	165	137	342

Figure S100. Get High-res Image Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 14(11p13) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.5e-05 (Fisher's exact test), Q value = 0.009

Table S101. Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 14(11P13) MUTATED	28	78	76
AMP PEAK 14(11P13) WILD-TYPE	172	345	173

Figure S101. Get High-res Image Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 14(11p13) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.39e-05 (Fisher's exact test), Q value = 0.0039

Table S102. Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 14(11P13) MUTATED	61	101	20
AMP PEAK 14(11P13) WILD-TYPE	143	508	39

Figure S102. Get High-res Image Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 15(11q13.3) mutation analysis' versus 'CN_CNMF'

P value = 6.2e-34 (Chi-square test), Q value = 3.8e-31

Table S103. Gene #15: 'Amp Peak 15(11q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 15(11Q13.3) MUTATED	63	29	145	83	20
AMP PEAK 15(11Q13.3) WILD-TYPE	283	47	53	132	36

Figure S103. Get High-res Image Gene #15: 'Amp Peak 15(11q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 15(11q13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.83e-08 (Chi-square test), Q value = 6.9e-06

Table S104. Gene #15: 'Amp Peak 15(11q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 15(11Q13.3) MUTATED	34	35	41	67	11	18
AMP PEAK 15(11Q13.3) WILD-TYPE	62	107	39	56	25	72

Figure S104. Get High-res Image Gene #15: 'Amp Peak 15(11q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 16(11q14.1) mutation analysis' versus 'CN_CNMF'

P value = 4.58e-13 (Chi-square test), Q value = 2.2e-10

Table S105. Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 16(11Q14.1) MUTATED	39	17	71	79	14
AMP PEAK 16(11Q14.1) WILD-TYPE	307	59	127	136	42

Figure S105. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 16(11q14.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.14e-05 (Chi-square test), Q value = 0.0083

Table S106. Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 16(11Q14.1) MUTATED	33	20	30	25	6	13
AMP PEAK 16(11Q14.1) WILD-TYPE	63	122	50	98	30	77

Figure S106. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 16(11q14.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000112 (Fisher's exact test), Q value = 0.026

Table S107. Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 16(11Q14.1) MUTATED	83	27	100
AMP PEAK 16(11Q14.1) WILD-TYPE	152	128	334

Figure S107. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 16(11q14.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.23

Table S108. Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 16(11Q14.1) MUTATED	97	44	69
AMP PEAK 16(11Q14.1) WILD-TYPE	316	172	126

Figure S108. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 16(11q14.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.64e-07 (Fisher's exact test), Q value = 0.00015

Table S109. Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 16(11Q14.1) MUTATED	32	89	91
AMP PEAK 16(11Q14.1) WILD-TYPE	168	334	158

Figure S109. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 16(11q14.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.01e-05 (Fisher's exact test), Q value = 0.017

Table S110. Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 16(11Q14.1) MUTATED	66	123	23
AMP PEAK 16(11Q14.1) WILD-TYPE	138	486	36

Figure S110. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 17(12p13.33) mutation analysis' versus 'MRNA_CNMF'

P value = 1.74e-10 (Fisher's exact test), Q value = 7.4e-08

Table S111. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 17(12P13.33) MUTATED	53	14	77
AMP PEAK 17(12P13.33) WILD-TYPE	203	78	82

Figure S111. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 17(12p13.33) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.35e-13 (Fisher's exact test), Q value = 6.6e-11

Table S112. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 17(12P13.33) MUTATED	61	72	11
AMP PEAK 17(12P13.33) WILD-TYPE	60	180	123

Figure S112. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 17(12p13.33) mutation analysis' versus 'CN_CNMF'

P value = 3.32e-28 (Chi-square test), Q value = 2e-25

Table S113. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 17(12P13.33) MUTATED	23	22	64	107	16
AMP PEAK 17(12P13.33) WILD-TYPE	323	54	134	108	40

Figure S113. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 17(12p13.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.4e-15 (Chi-square test), Q value = 2.2e-12

Table S114. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 17(12P13.33) MUTATED	49	13	19	40	2	10
AMP PEAK 17(12P13.33) WILD-TYPE	47	129	61	83	34	80

Figure S114. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 17(12p13.33) mutation analysis' versus 'RPPA_CNMF'

P value = 6.79e-08 (Fisher's exact test), Q value = 2.4e-05

Table S115. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
AMP PEAK 17(12P13.33) MUTATED	68	30	18
AMP PEAK 17(12P13.33) WILD-TYPE	78	99	97

Figure S115. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 17(12p13.33) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 3.08e-07 (Fisher's exact test), Q value = 1e-04

Table S116. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
AMP PEAK 17(12P13.33) MUTATED	41	16	59
AMP PEAK 17(12P13.33) WILD-TYPE	115	92	67

Figure S116. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 17(12p13.33) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.79e-17 (Fisher's exact test), Q value = 9.7e-15

Table S117. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 17(12P13.33) MUTATED	106	12	95
AMP PEAK 17(12P13.33) WILD-TYPE	129	143	339

Figure S117. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 17(12p13.33) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.09e-15 (Fisher's exact test), Q value = 1.1e-12

Table S118. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 17(12P13.33) MUTATED	95	26	92
AMP PEAK 17(12P13.33) WILD-TYPE	318	190	103

Figure S118. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 17(12p13.33) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.16e-22 (Fisher's exact test), Q value = 2.4e-19

Table S119. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 17(12P13.33) MUTATED	26	75	123
AMP PEAK 17(12P13.33) WILD-TYPE	174	348	126

Figure S119. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 17(12p13.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.45e-19 (Fisher's exact test), Q value = 1.9e-16

Table S120. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 17(12P13.33) MUTATED	104	105	15
AMP PEAK 17(12P13.33) WILD-TYPE	100	504	44

Figure S120. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.75e-06 (Fisher's exact test), Q value = 0.00055

Table S121. Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 18(12Q15) MUTATED	72	10	64
AMP PEAK 18(12Q15) WILD-TYPE	184	82	95

Figure S121. Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 6.29e-08 (Fisher's exact test), Q value = 2.3e-05

Table S122. Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 18(12Q15) MUTATED	28	100	18
AMP PEAK 18(12Q15) WILD-TYPE	93	152	116

Figure S122. Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.6e-25 (Chi-square test), Q value = 9.4e-23

Table S123. Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 18(12Q15) MUTATED	30	25	101	60	12
AMP PEAK 18(12Q15) WILD-TYPE	316	51	97	155	44

Figure S123. Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.64e-13 (Chi-square test), Q value = 8e-11

Table S124. Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 18(12Q15) MUTATED	17	19	17	62	6	10
AMP PEAK 18(12Q15) WILD-TYPE	79	123	63	61	30	80

Figure S124. Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0033

Table S125. Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 18(12Q15) MUTATED	61	20	138
AMP PEAK 18(12Q15) WILD-TYPE	174	135	296

Figure S125. Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 6.14e-09 (Fisher's exact test), Q value = 2.4e-06

Table S126. Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 18(12Q15) MUTATED	21	115	85
AMP PEAK 18(12Q15) WILD-TYPE	179	308	164

Figure S126. Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 9.35e-06 (Chi-square test), Q value = 0.0027

Table S127. Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 19(13Q12.3) MUTATED	22	15	34	44	10
AMP PEAK 19(13Q12.3) WILD-TYPE	324	61	164	171	46

Figure S127. Get High-res Image Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.18e-06 (Fisher's exact test), Q value = 0.00067

Table S128. Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 19(13Q12.3) MUTATED	45	5	70
AMP PEAK 19(13Q12.3) WILD-TYPE	190	150	364

Figure S128. Get High-res Image Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3.53e-06 (Fisher's exact test), Q value = 0.0011

Table S129. Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 19(13Q12.3) MUTATED	12	54	55
AMP PEAK 19(13Q12.3) WILD-TYPE	188	369	194

Figure S129. Get High-res Image Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 20(13q34) mutation analysis' versus 'MRNA_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.21

Table S130. Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 20(13Q34) MUTATED	35	15	45
AMP PEAK 20(13Q34) WILD-TYPE	221	77	114

Figure S130. Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 20(13q34) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 8.57e-10 (Fisher's exact test), Q value = 3.5e-07

Table S131. Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 20(13Q34) MUTATED	46	40	9
AMP PEAK 20(13Q34) WILD-TYPE	75	212	125

Figure S131. Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 20(13q34) mutation analysis' versus 'CN_CNMF'

P value = 1.9e-20 (Chi-square test), Q value = 1.1e-17

Table S132. Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 20(13Q34) MUTATED	26	11	28	85	7
AMP PEAK 20(13Q34) WILD-TYPE	320	65	170	130	49

Figure S132. Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 20(13q34) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.37e-12 (Chi-square test), Q value = 1.1e-09

Table S133. Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 20(13Q34) MUTATED	40	9	11	18	1	11
AMP PEAK 20(13Q34) WILD-TYPE	56	133	69	105	35	79

Figure S133. Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 20(13q34) mutation analysis' versus 'RPPA_CNMF'

P value = 4.1e-06 (Fisher's exact test), Q value = 0.0012

Table S134. Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
AMP PEAK 20(13Q34) MUTATED	48	22	10
AMP PEAK 20(13Q34) WILD-TYPE	98	107	105

Figure S134. Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 20(13q34) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.88e-08 (Fisher's exact test), Q value = 1.1e-05

Table S135. Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
AMP PEAK 20(13Q34) MUTATED	25	8	47
AMP PEAK 20(13Q34) WILD-TYPE	131	100	79

Figure S135. Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 20(13q34) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.54e-16 (Fisher's exact test), Q value = 1.9e-13

Table S136. Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 20(13Q34) MUTATED	79	5	58
AMP PEAK 20(13Q34) WILD-TYPE	156	150	376

Figure S136. Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 20(13q34) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.05e-15 (Fisher's exact test), Q value = 1.5e-12

Table S137. Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 20(13Q34) MUTATED	51	18	73
AMP PEAK 20(13Q34) WILD-TYPE	362	198	122

Figure S137. Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(13q34) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.36e-15 (Fisher's exact test), Q value = 1.2e-12

Table S138. Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 20(13Q34) MUTATED	24	42	87
AMP PEAK 20(13Q34) WILD-TYPE	176	381	162

Figure S138. Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 20(13q34) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.26e-19 (Fisher's exact test), Q value = 7e-17

Table S139. Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 20(13Q34) MUTATED	81	59	13
AMP PEAK 20(13Q34) WILD-TYPE	123	550	46

Figure S139. Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 21(14q21.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.091

Table S140. Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 21(14Q21.1) MUTATED	18	73	19
AMP PEAK 21(14Q21.1) WILD-TYPE	103	179	115

Figure S140. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 21(14q21.1) mutation analysis' versus 'CN_CNMF'

P value = 1.03e-13 (Chi-square test), Q value = 5e-11

Table S141. Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 21(14Q21.1) MUTATED	31	19	75	43	11
AMP PEAK 21(14Q21.1) WILD-TYPE	315	57	123	172	45

Figure S141. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 21(14q21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.91e-06 (Chi-square test), Q value = 0.0012

Table S142. Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 21(14Q21.1) MUTATED	14	17	24	38	4	7
AMP PEAK 21(14Q21.1) WILD-TYPE	82	125	56	85	32	83

Figure S142. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 21(14q21.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.65e-05 (Fisher's exact test), Q value = 0.0045

Table S143. Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 21(14Q21.1) MUTATED	41	16	116
AMP PEAK 21(14Q21.1) WILD-TYPE	194	139	318

Figure S143. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 21(14q21.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.23

Table S144. Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 21(14Q21.1) MUTATED	108	36	29
AMP PEAK 21(14Q21.1) WILD-TYPE	305	180	166

Figure S144. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 21(14q21.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.026

Table S145. Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 21(14Q21.1) MUTATED	20	92	61
AMP PEAK 21(14Q21.1) WILD-TYPE	180	331	188

Figure S145. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MRNA_CNMF'

P value = 3.16e-07 (Fisher's exact test), Q value = 0.00011

Table S146. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 22(15Q26.3) MUTATED	36	10	55
AMP PEAK 22(15Q26.3) WILD-TYPE	220	82	104

Figure S146. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000286 (Fisher's exact test), Q value = 0.062

Table S147. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 22(15Q26.3) MUTATED	38	48	15
AMP PEAK 22(15Q26.3) WILD-TYPE	83	204	119

Figure S147. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 22(15q26.3) mutation analysis' versus 'CN_CNMF'

P value = 2.36e-14 (Chi-square test), Q value = 1.2e-11

Table S148. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 22(15Q26.3) MUTATED	29	8	44	75	6
AMP PEAK 22(15Q26.3) WILD-TYPE	317	68	154	140	50

Figure S148. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00091 (Chi-square test), Q value = 0.18

Table S149. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 22(15Q26.3) MUTATED	24	7	14	25	6	14
AMP PEAK 22(15Q26.3) WILD-TYPE	72	135	66	98	30	76

Figure S149. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.038

Table S150. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
AMP PEAK 22(15Q26.3) MUTATED	46	17	16
AMP PEAK 22(15Q26.3) WILD-TYPE	100	112	99

Figure S150. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.25e-08 (Fisher's exact test), Q value = 1.9e-05

Table S151. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 22(15Q26.3) MUTATED	69	11	72
AMP PEAK 22(15Q26.3) WILD-TYPE	166	144	362

Figure S151. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.29e-05 (Fisher's exact test), Q value = 0.0087

Table S152. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 22(15Q26.3) MUTATED	65	29	58
AMP PEAK 22(15Q26.3) WILD-TYPE	348	187	137

Figure S152. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.37e-07 (Fisher's exact test), Q value = 4.8e-05

Table S153. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 22(15Q26.3) MUTATED	25	56	74
AMP PEAK 22(15Q26.3) WILD-TYPE	175	367	175

Figure S153. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.18e-10 (Fisher's exact test), Q value = 1.7e-07

Table S154. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 22(15Q26.3) MUTATED	68	75	12
AMP PEAK 22(15Q26.3) WILD-TYPE	136	534	47

Figure S154. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(17p11.2) mutation analysis' versus 'CN_CNMF'

P value = 7.6e-07 (Chi-square test), Q value = 0.00025

Table S155. Gene #23: 'Amp Peak 23(17p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 23(17P11.2) MUTATED	25	14	44	26	15
AMP PEAK 23(17P11.2) WILD-TYPE	321	62	154	189	41

Figure S155. Get High-res Image Gene #23: 'Amp Peak 23(17p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000108 (Fisher's exact test), Q value = 0.026

Table S156. Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 24(17Q12) MUTATED	77	16	68
AMP PEAK 24(17Q12) WILD-TYPE	179	76	91

Figure S156. Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 1.51e-05 (Fisher's exact test), Q value = 0.0042

Table S157. Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 24(17Q12) MUTATED	37	101	23
AMP PEAK 24(17Q12) WILD-TYPE	84	151	111

Figure S157. Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 9.14e-37 (Chi-square test), Q value = 5.6e-34

Table S158. Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 24(17Q12) MUTATED	58	24	138	48	21
AMP PEAK 24(17Q12) WILD-TYPE	288	52	60	167	35

Figure S158. 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 = 8.72e-08 (Chi-square test), Q value = 3.1e-05

Table S159. Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 24(17Q12) MUTATED	25	30	35	63	11	18
AMP PEAK 24(17Q12) WILD-TYPE	71	112	45	60	25	72

Figure S159. 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 'MRNASEQ_CNMF'

P value = 6.59e-05 (Fisher's exact test), Q value = 0.016

Table S160. Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 24(17Q12) MUTATED	88	29	156
AMP PEAK 24(17Q12) WILD-TYPE	147	126	278

Figure S160. 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 'MIRSEQ_CHIERARCHICAL'

P value = 0.000416 (Fisher's exact test), Q value = 0.089

Table S161. Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 24(17Q12) MUTATED	66	183	33
AMP PEAK 24(17Q12) WILD-TYPE	138	426	26

Figure S161. 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 'MRNA_CNMF'

P value = 0.000367 (Fisher's exact test), Q value = 0.079

Table S162. Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 25(17Q23.1) MUTATED	107	23	80
AMP PEAK 25(17Q23.1) WILD-TYPE	149	69	79

Figure S162. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 5.11e-05 (Fisher's exact test), Q value = 0.013

Table S163. Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 25(17Q23.1) MUTATED	46	127	37
AMP PEAK 25(17Q23.1) WILD-TYPE	75	125	97

Figure S163. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 4.12e-40 (Chi-square test), Q value = 2.5e-37

Table S164. Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 25(17Q23.1) MUTATED	69	23	158	93	24
AMP PEAK 25(17Q23.1) WILD-TYPE	277	53	40	122	32

Figure S164. 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 = 4.73e-09 (Chi-square test), Q value = 1.9e-06

Table S165. Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 25(17Q23.1) MUTATED	37	37	36	78	16	24
AMP PEAK 25(17Q23.1) WILD-TYPE	59	105	44	45	20	66

Figure S165. 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 'MRNASEQ_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.044

Table S166. Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 25(17Q23.1) MUTATED	98	44	205
AMP PEAK 25(17Q23.1) WILD-TYPE	137	111	229

Figure S166. 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 'MIRSEQ_CNMF'

P value = 1.72e-06 (Fisher's exact test), Q value = 0.00054

Table S167. Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 25(17Q23.1) MUTATED	60	165	133
AMP PEAK 25(17Q23.1) WILD-TYPE	140	258	116

Figure S167. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'MRNA_CNMF'

P value = 5.61e-08 (Fisher's exact test), Q value = 2e-05

Table S168. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 26(19Q12) MUTATED	44	26	69
AMP PEAK 26(19Q12) WILD-TYPE	212	66	90

Figure S168. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.55e-12 (Fisher's exact test), Q value = 2.5e-09

Table S169. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 26(19Q12) MUTATED	64	56	19
AMP PEAK 26(19Q12) WILD-TYPE	57	196	115

Figure S169. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 26(19q12) mutation analysis' versus 'CN_CNMF'

P value = 1.81e-24 (Chi-square test), Q value = 1.1e-21

Table S170. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 26(19Q12) MUTATED	35	28	44	108	16
AMP PEAK 26(19Q12) WILD-TYPE	311	48	154	107	40

Figure S170. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.37e-08 (Chi-square test), Q value = 5.2e-06

Table S171. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 26(19Q12) MUTATED	46	17	17	31	4	21
AMP PEAK 26(19Q12) WILD-TYPE	50	125	63	92	32	69

Figure S171. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'RPPA_CNMF'

P value = 6.56e-07 (Fisher's exact test), Q value = 0.00022

Table S172. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
AMP PEAK 26(19Q12) MUTATED	64	23	22
AMP PEAK 26(19Q12) WILD-TYPE	82	106	93

Figure S172. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.00048

Table S173. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
AMP PEAK 26(19Q12) MUTATED	29	23	57
AMP PEAK 26(19Q12) WILD-TYPE	127	85	69

Figure S173. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 26(19q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.87e-14 (Fisher's exact test), Q value = 1.9e-11

Table S174. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 26(19Q12) MUTATED	107	27	80
AMP PEAK 26(19Q12) WILD-TYPE	128	128	354

Figure S174. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.67e-17 (Fisher's exact test), Q value = 2.5e-14

Table S175. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
AMP PEAK 26(19Q12) MUTATED	75	40	99
AMP PEAK 26(19Q12) WILD-TYPE	338	176	96

Figure S175. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(19q12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.36e-12 (Fisher's exact test), Q value = 1.1e-09

Table S176. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 26(19Q12) MUTATED	43	75	108
AMP PEAK 26(19Q12) WILD-TYPE	157	348	141

Figure S176. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.69e-17 (Fisher's exact test), Q value = 9.2e-15

Table S177. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 26(19Q12) MUTATED	101	107	18
AMP PEAK 26(19Q12) WILD-TYPE	103	502	41

Figure S177. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 27(19q13.42) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.045

Table S178. Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 27(19Q13.42) MUTATED	54	22	63
AMP PEAK 27(19Q13.42) WILD-TYPE	202	70	96

Figure S178. Get High-res Image Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 27(19q13.42) mutation analysis' versus 'CN_CNMF'

P value = 5.8e-15 (Chi-square test), Q value = 2.9e-12

Table S179. Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 27(19Q13.42) MUTATED	38	29	62	87	16
AMP PEAK 27(19Q13.42) WILD-TYPE	308	47	136	128	40

Figure S179. Get High-res Image Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 27(19q13.42) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.71e-06 (Chi-square test), Q value = 0.0014

Table S180. Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 27(19Q13.42) MUTATED	31	18	22	48	5	16
AMP PEAK 27(19Q13.42) WILD-TYPE	65	124	58	75	31	74

Figure S180. Get High-res Image Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 27(19q13.42) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0051

Table S181. Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 27(19Q13.42) MUTATED	36	100	91
AMP PEAK 27(19Q13.42) WILD-TYPE	164	323	158

Figure S181. Get High-res Image Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 27(19q13.42) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.44e-05 (Fisher's exact test), Q value = 0.022

Table S182. Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 27(19Q13.42) MUTATED	71	133	23
AMP PEAK 27(19Q13.42) WILD-TYPE	133	476	36

Figure S182. Get High-res Image Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(20q13.2) mutation analysis' versus 'MRNA_CNMF'

P value = 2.58e-08 (Fisher's exact test), Q value = 9.5e-06

Table S183. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
AMP PEAK 28(20Q13.2) MUTATED	128	30	111
AMP PEAK 28(20Q13.2) WILD-TYPE	128	62	48

Figure S183. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.22e-06 (Fisher's exact test), Q value = 0.00039

Table S184. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
AMP PEAK 28(20Q13.2) MUTATED	67	156	46
AMP PEAK 28(20Q13.2) WILD-TYPE	54	96	88

Figure S184. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 28(20q13.2) mutation analysis' versus 'CN_CNMF'

P value = 3.23e-49 (Chi-square test), Q value = 2e-46

Table S185. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
AMP PEAK 28(20Q13.2) MUTATED	71	44	163	146	31
AMP PEAK 28(20Q13.2) WILD-TYPE	275	32	35	69	25

Figure S185. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.07e-20 (Chi-square test), Q value = 1.2e-17

Table S186. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
AMP PEAK 28(20Q13.2) MUTATED	56	35	44	100	12	30
AMP PEAK 28(20Q13.2) WILD-TYPE	40	107	36	23	24	60

Figure S186. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000494 (Fisher's exact test), Q value = 0.1

Table S187. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
AMP PEAK 28(20Q13.2) MUTATED	98	65	51
AMP PEAK 28(20Q13.2) WILD-TYPE	48	64	64

Figure S187. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.17e-09 (Fisher's exact test), Q value = 4.8e-07

Table S188. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
AMP PEAK 28(20Q13.2) MUTATED	138	46	250
AMP PEAK 28(20Q13.2) WILD-TYPE	97	109	184

Figure S188. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.02e-11 (Fisher's exact test), Q value = 1.4e-08

Table S189. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
AMP PEAK 28(20Q13.2) MUTATED	67	215	165
AMP PEAK 28(20Q13.2) WILD-TYPE	133	208	84

Figure S189. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.29e-08 (Fisher's exact test), Q value = 8.6e-06

Table S190. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
AMP PEAK 28(20Q13.2) MUTATED	117	281	49
AMP PEAK 28(20Q13.2) WILD-TYPE	87	328	10

Figure S190. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 3.17e-06 (Fisher's exact test), Q value = 0.00096

Table S191. Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 1(1P36.13) MUTATED	50	132	35
DEL PEAK 1(1P36.13) WILD-TYPE	71	120	99

Figure S191. Get High-res Image Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 3e-33 (Chi-square test), Q value = 1.8e-30

Table S192. Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 1(1P36.13) MUTATED	60	52	129	109	23
DEL PEAK 1(1P36.13) WILD-TYPE	286	24	69	106	33

Figure S192. Get High-res Image Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 6.69e-08 (Chi-square test), Q value = 2.4e-05

Table S193. Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 1(1P36.13) MUTATED	41	39	45	69	10	23
DEL PEAK 1(1P36.13) WILD-TYPE	55	103	35	54	26	67

Figure S193. Get High-res Image Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 4.33e-06 (Fisher's exact test), Q value = 0.0013

Table S194. Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 1(1P36.13) MUTATED	104	39	206
DEL PEAK 1(1P36.13) WILD-TYPE	131	116	228

Figure S194. Get High-res Image Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3.4e-11 (Fisher's exact test), Q value = 1.5e-08

Table S195. Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 1(1P36.13) MUTATED	45	179	135
DEL PEAK 1(1P36.13) WILD-TYPE	155	244	114

Figure S195. Get High-res Image Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 2(1p21.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000109 (Fisher's exact test), Q value = 0.026

Table S196. Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 2(1P21.2) MUTATED	31	111	35
DEL PEAK 2(1P21.2) WILD-TYPE	90	141	99

Figure S196. Get High-res Image Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p21.2) mutation analysis' versus 'CN_CNMF'

P value = 4.04e-23 (Chi-square test), Q value = 2.3e-20

Table S197. Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 2(1P21.2) MUTATED	60	51	104	69	17
DEL PEAK 2(1P21.2) WILD-TYPE	286	25	94	146	39

Figure S197. Get High-res Image Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 2(1p21.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.77e-05 (Chi-square test), Q value = 0.021

Table S198. Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 2(1P21.2) MUTATED	28	33	38	53	11	19
DEL PEAK 2(1P21.2) WILD-TYPE	68	109	42	70	25	71

Figure S198. Get High-res Image Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 2(1p21.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000366 (Fisher's exact test), Q value = 0.079

Table S199. Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 2(1P21.2) MUTATED	70	38	175
DEL PEAK 2(1P21.2) WILD-TYPE	165	117	259

Figure S199. Get High-res Image Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 7.69e-07 (Fisher's exact test), Q value = 0.00025

Table S200. Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 3(2Q37.3) MUTATED	65	19	76
DEL PEAK 3(2Q37.3) WILD-TYPE	191	73	83

Figure S200. Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 5.89e-09 (Fisher's exact test), Q value = 2.3e-06

Table S201. Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 3(2Q37.3) MUTATED	58	84	18
DEL PEAK 3(2Q37.3) WILD-TYPE	63	168	116

Figure S201. Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 5.27e-20 (Chi-square test), Q value = 3e-17

Table S202. Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 3(2Q37.3) MUTATED	40	29	69	103	22
DEL PEAK 3(2Q37.3) WILD-TYPE	306	47	129	112	34

Figure S202. Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 4.74e-10 (Chi-square test), Q value = 2e-07

Table S203. Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 3(2Q37.3) MUTATED	43	21	24	48	4	10
DEL PEAK 3(2Q37.3) WILD-TYPE	53	121	56	75	32	80

Figure S203. Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.32e-08 (Fisher's exact test), Q value = 5e-06

Table S204. Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 3(2Q37.3) MUTATED	70	37	16
DEL PEAK 3(2Q37.3) WILD-TYPE	76	92	99

Figure S204. Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 1.53e-07 (Fisher's exact test), Q value = 5.3e-05

Table S205. Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 3(2Q37.3) MUTATED	55	13	55
DEL PEAK 3(2Q37.3) WILD-TYPE	101	95	71

Figure S205. Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 3.19e-11 (Fisher's exact test), Q value = 1.4e-08

Table S206. Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 3(2Q37.3) MUTATED	102	18	126
DEL PEAK 3(2Q37.3) WILD-TYPE	133	137	308

Figure S206. Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 2.2e-07 (Fisher's exact test), Q value = 7.6e-05

Table S207. Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 3(2Q37.3) MUTATED	128	37	81
DEL PEAK 3(2Q37.3) WILD-TYPE	285	179	114

Figure S207. Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.3e-12 (Fisher's exact test), Q value = 1.5e-09

Table S208. Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 3(2Q37.3) MUTATED	31	110	114
DEL PEAK 3(2Q37.3) WILD-TYPE	169	313	135

Figure S208. Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 2.58e-07 (Fisher's exact test), Q value = 8.8e-05

Table S209. Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 3(2Q37.3) MUTATED	84	144	27
DEL PEAK 3(2Q37.3) WILD-TYPE	120	465	32

Figure S209. Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(3p14.3) mutation analysis' versus 'MRNA_CNMF'

P value = 2.23e-13 (Fisher's exact test), Q value = 1.1e-10

Table S210. Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 4(3P14.3) MUTATED	49	27	88
DEL PEAK 4(3P14.3) WILD-TYPE	207	65	71

Figure S210. Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 8.42e-09 (Fisher's exact test), Q value = 3.3e-06

Table S211. Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 4(3P14.3) MUTATED	67	66	31
DEL PEAK 4(3P14.3) WILD-TYPE	54	186	103

Figure S211. Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 4(3p14.3) mutation analysis' versus 'CN_CNMF'

P value = 2.26e-32 (Chi-square test), Q value = 1.4e-29

Table S212. Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 4(3P14.3) MUTATED	47	11	75	130	11
DEL PEAK 4(3P14.3) WILD-TYPE	299	65	123	85	45

Figure S212. Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.65e-12 (Chi-square test), Q value = 2.1e-09

Table S213. Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 4(3P14.3) MUTATED	48	12	31	46	12	17
DEL PEAK 4(3P14.3) WILD-TYPE	48	130	49	77	24	73

Figure S213. Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'RPPA_CNMF'

P value = 2.21e-09 (Fisher's exact test), Q value = 8.8e-07

Table S214. Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 4(3P14.3) MUTATED	79	25	32
DEL PEAK 4(3P14.3) WILD-TYPE	67	104	83

Figure S214. Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.0034

Table S215. Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 4(3P14.3) MUTATED	40	31	65
DEL PEAK 4(3P14.3) WILD-TYPE	116	77	61

Figure S215. Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 4(3p14.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.63e-16 (Fisher's exact test), Q value = 8.7e-14

Table S216. Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 4(3P14.3) MUTATED	125	28	105
DEL PEAK 4(3P14.3) WILD-TYPE	110	127	329

Figure S216. Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.37e-11 (Fisher's exact test), Q value = 2.4e-08

Table S217. Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 4(3P14.3) MUTATED	103	54	101
DEL PEAK 4(3P14.3) WILD-TYPE	310	162	94

Figure S217. Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 4(3p14.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.81e-20 (Fisher's exact test), Q value = 5.5e-17

Table S218. Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 4(3P14.3) MUTATED	44	88	135
DEL PEAK 4(3P14.3) WILD-TYPE	156	335	114

Figure S218. Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.27e-14 (Fisher's exact test), Q value = 1.1e-11

Table S219. Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 4(3P14.3) MUTATED	105	137	25
DEL PEAK 4(3P14.3) WILD-TYPE	99	472	34

Figure S219. Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.39e-10 (Fisher's exact test), Q value = 6e-08

Table S220. Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 5(4P16.3) MUTATED	53	31	84
DEL PEAK 5(4P16.3) WILD-TYPE	203	61	75

Figure S220. Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.16e-12 (Fisher's exact test), Q value = 1.5e-09

Table S221. Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 5(4P16.3) MUTATED	72	72	24
DEL PEAK 5(4P16.3) WILD-TYPE	49	180	110

Figure S221. Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(4p16.3) mutation analysis' versus 'CN_CNMF'

P value = 2.46e-27 (Chi-square test), Q value = 1.5e-24

Table S222. Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 5(4P16.3) MUTATED	49	39	53	123	15
DEL PEAK 5(4P16.3) WILD-TYPE	297	37	145	92	41

Figure S222. Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.82e-12 (Chi-square test), Q value = 4e-09

Table S223. Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 5(4P16.3) MUTATED	58	28	26	27	5	21
DEL PEAK 5(4P16.3) WILD-TYPE	38	114	54	96	31	69

Figure S223. Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'RPPA_CNMF'

P value = 6.65e-07 (Fisher's exact test), Q value = 0.00022

Table S224. Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 5(4P16.3) MUTATED	75	39	24
DEL PEAK 5(4P16.3) WILD-TYPE	71	90	91

Figure S224. Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 3.22e-06 (Fisher's exact test), Q value = 0.00097

Table S225. Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 5(4P16.3) MUTATED	48	24	66
DEL PEAK 5(4P16.3) WILD-TYPE	108	84	60

Figure S225. Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 5(4p16.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.72e-22 (Fisher's exact test), Q value = 1.6e-19

Table S226. Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 5(4P16.3) MUTATED	133	22	104
DEL PEAK 5(4P16.3) WILD-TYPE	102	133	330

Figure S226. Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.6e-18 (Fisher's exact test), Q value = 3.1e-15

Table S227. Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 5(4P16.3) MUTATED	110	38	111
DEL PEAK 5(4P16.3) WILD-TYPE	303	178	84

Figure S227. Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.12e-14 (Fisher's exact test), Q value = 5.6e-12

Table S228. Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 5(4P16.3) MUTATED	40	103	127
DEL PEAK 5(4P16.3) WILD-TYPE	160	320	122

Figure S228. Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.71e-15 (Fisher's exact test), Q value = 1.9e-12

Table S229. Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 5(4P16.3) MUTATED	108	138	24
DEL PEAK 5(4P16.3) WILD-TYPE	96	471	35

Figure S229. Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2) mutation analysis' versus 'MRNA_CNMF'

P value = 7.12e-10 (Fisher's exact test), Q value = 2.9e-07

Table S230. Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 6(4Q35.2) MUTATED	55	26	83
DEL PEAK 6(4Q35.2) WILD-TYPE	201	66	76

Figure S230. Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.92e-07 (Fisher's exact test), Q value = 6.7e-05

Table S231. Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 6(4Q35.2) MUTATED	63	74	27
DEL PEAK 6(4Q35.2) WILD-TYPE	58	178	107

Figure S231. Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 6(4q35.2) mutation analysis' versus 'CN_CNMF'

P value = 7.04e-36 (Chi-square test), Q value = 4.3e-33

Table S232. Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 6(4Q35.2) MUTATED	50	41	44	134	11
DEL PEAK 6(4Q35.2) WILD-TYPE	296	35	154	81	45

Figure S232. Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.96e-14 (Chi-square test), Q value = 2.9e-11

Table S233. Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 6(4Q35.2) MUTATED	61	26	24	23	7	25
DEL PEAK 6(4Q35.2) WILD-TYPE	35	116	56	100	29	65

Figure S233. Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'RPPA_CNMF'

P value = 3.47e-08 (Fisher's exact test), Q value = 1.3e-05

Table S234. Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 6(4Q35.2) MUTATED	77	34	24
DEL PEAK 6(4Q35.2) WILD-TYPE	69	95	91

Figure S234. Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.09e-06 (Fisher's exact test), Q value = 0.00065

Table S235. Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 6(4Q35.2) MUTATED	44	25	66
DEL PEAK 6(4Q35.2) WILD-TYPE	112	83	60

Figure S235. Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 6(4q35.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.04e-21 (Fisher's exact test), Q value = 1.7e-18

Table S236. Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 6(4Q35.2) MUTATED	131	22	105
DEL PEAK 6(4Q35.2) WILD-TYPE	104	133	329

Figure S236. Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-15 (Fisher's exact test), Q value = 6.1e-13

Table S237. Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 6(4Q35.2) MUTATED	108	42	108
DEL PEAK 6(4Q35.2) WILD-TYPE	305	174	87

Figure S237. Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1e-15 (Fisher's exact test), Q value = 5.2e-13

Table S238. Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 6(4Q35.2) MUTATED	38	102	128
DEL PEAK 6(4Q35.2) WILD-TYPE	162	321	121

Figure S238. Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.34e-17 (Fisher's exact test), Q value = 1.3e-14

Table S239. Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 6(4Q35.2) MUTATED	111	133	24
DEL PEAK 6(4Q35.2) WILD-TYPE	93	476	35

Figure S239. Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2) mutation analysis' versus 'MRNA_CNMF'

P value = 8.07e-22 (Fisher's exact test), Q value = 4.6e-19

Table S240. Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 7(5Q11.2) MUTATED	26	22	86
DEL PEAK 7(5Q11.2) WILD-TYPE	230	70	73

Figure S240. Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.58e-26 (Fisher's exact test), Q value = 3.3e-23

Table S241. Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 7(5Q11.2) MUTATED	79	41	14
DEL PEAK 7(5Q11.2) WILD-TYPE	42	211	120

Figure S241. Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 7(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 3.42e-62 (Chi-square test), Q value = 2.1e-59

Table S242. Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 7(5Q11.2) MUTATED	31	6	29	150	15
DEL PEAK 7(5Q11.2) WILD-TYPE	315	70	169	65	41

Figure S242. Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.27e-36 (Chi-square test), Q value = 2e-33

Table S243. Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 7(5Q11.2) MUTATED	72	3	14	26	4	21
DEL PEAK 7(5Q11.2) WILD-TYPE	24	139	66	97	32	69

Figure S243. Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'RPPA_CNMF'

P value = 1.99e-15 (Fisher's exact test), Q value = 1e-12

Table S244. Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 7(5Q11.2) MUTATED	77	13	23
DEL PEAK 7(5Q11.2) WILD-TYPE	69	116	92

Figure S244. Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.27e-18 (Fisher's exact test), Q value = 7e-16

Table S245. Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 7(5Q11.2) MUTATED	25	13	75
DEL PEAK 7(5Q11.2) WILD-TYPE	131	95	51

Figure S245. Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 7(5q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.1e-41 (Fisher's exact test), Q value = 1.9e-38

Table S246. Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 7(5Q11.2) MUTATED	141	11	66
DEL PEAK 7(5Q11.2) WILD-TYPE	94	144	368

Figure S246. Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.36e-44 (Fisher's exact test), Q value = 5.2e-41

Table S247. Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 7(5Q11.2) MUTATED	65	23	130
DEL PEAK 7(5Q11.2) WILD-TYPE	348	193	65

Figure S247. Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.02e-41 (Fisher's exact test), Q value = 3.7e-38

Table S248. Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 7(5Q11.2) MUTATED	28	48	144
DEL PEAK 7(5Q11.2) WILD-TYPE	172	375	105

Figure S248. Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.35e-49 (Fisher's exact test), Q value = 1.5e-46

Table S249. Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 7(5Q11.2) MUTATED	134	69	17
DEL PEAK 7(5Q11.2) WILD-TYPE	70	540	42

Figure S249. Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3) mutation analysis' versus 'MRNA_CNMF'

P value = 5.18e-25 (Fisher's exact test), Q value = 3e-22

Table S250. Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 8(5Q21.3) MUTATED	23	22	89
DEL PEAK 8(5Q21.3) WILD-TYPE	233	70	70

Figure S250. Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.83e-27 (Fisher's exact test), Q value = 1.1e-24

Table S251. Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 8(5Q21.3) MUTATED	80	42	12
DEL PEAK 8(5Q21.3) WILD-TYPE	41	210	122

Figure S251. Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 8(5q21.3) mutation analysis' versus 'CN_CNMF'

P value = 2.4e-74 (Chi-square test), Q value = 1.5e-71

Table S252. Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 8(5Q21.3) MUTATED	23	6	25	156	13
DEL PEAK 8(5Q21.3) WILD-TYPE	323	70	173	59	43

Figure S252. Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.41e-50 (Chi-square test), Q value = 8.8e-48

Table S253. Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 8(5Q21.3) MUTATED	80	2	9	21	2	21
DEL PEAK 8(5Q21.3) WILD-TYPE	16	140	71	102	34	69

Figure S253. Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'RPPA_CNMF'

P value = 5.76e-15 (Fisher's exact test), Q value = 2.9e-12

Table S254. Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 8(5Q21.3) MUTATED	76	13	23
DEL PEAK 8(5Q21.3) WILD-TYPE	70	116	92

Figure S254. Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.82e-15 (Fisher's exact test), Q value = 1.4e-12

Table S255. Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 8(5Q21.3) MUTATED	26	15	71
DEL PEAK 8(5Q21.3) WILD-TYPE	130	93	55

Figure S255. Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 8(5q21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.89e-48 (Fisher's exact test), Q value = 1.8e-45

Table S256. Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 8(5Q21.3) MUTATED	144	8	57
DEL PEAK 8(5Q21.3) WILD-TYPE	91	147	377

Figure S256. Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.1e-49 (Fisher's exact test), Q value = 3.2e-46

Table S257. Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 8(5Q21.3) MUTATED	55	22	132
DEL PEAK 8(5Q21.3) WILD-TYPE	358	194	63

Figure S257. Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.74e-40 (Fisher's exact test), Q value = 1.7e-37

Table S258. Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 8(5Q21.3) MUTATED	27	46	141
DEL PEAK 8(5Q21.3) WILD-TYPE	173	377	108

Figure S258. Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.29e-53 (Fisher's exact test), Q value = 1.4e-50

Table S259. Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 8(5Q21.3) MUTATED	136	63	15
DEL PEAK 8(5Q21.3) WILD-TYPE	68	546	44

Figure S259. Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.07e-06 (Chi-square test), Q value = 0.0012

Table S260. Gene #37: 'Del Peak 9(6p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 9(6P25.3) MUTATED	37	15	58	44	13
DEL PEAK 9(6P25.3) WILD-TYPE	309	61	140	171	43

Figure S260. Get High-res Image Gene #37: 'Del Peak 9(6p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 9(6p25.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.56e-05 (Chi-square test), Q value = 0.014

Table S261. Gene #37: 'Del Peak 9(6p25.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 9(6P25.3) MUTATED	23	16	16	39	2	11
DEL PEAK 9(6P25.3) WILD-TYPE	73	126	64	84	34	79

Figure S261. Get High-res Image Gene #37: 'Del Peak 9(6p25.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 10(6q15) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000985 (Fisher's exact test), Q value = 0.19

Table S262. Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 10(6Q15) MUTATED	25	100	43
DEL PEAK 10(6Q15) WILD-TYPE	96	152	91

Figure S262. Get High-res Image Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 10(6q15) mutation analysis' versus 'CN_CNMF'

P value = 1.45e-26 (Chi-square test), Q value = 8.6e-24

Table S263. Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 10(6Q15) MUTATED	78	25	117	37	36
DEL PEAK 10(6Q15) WILD-TYPE	268	51	81	178	20

Figure S263. Get High-res Image Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 10(6q15) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.07e-07 (Chi-square test), Q value = 3.8e-05

Table S264. Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 10(6Q15) MUTATED	19	49	27	64	6	17
DEL PEAK 10(6Q15) WILD-TYPE	77	93	53	59	30	73

Figure S264. Get High-res Image Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 10(6q15) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.0054

Table S265. Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 10(6Q15) MUTATED	55	46	176
DEL PEAK 10(6Q15) WILD-TYPE	180	109	258

Figure S265. Get High-res Image Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 10(6q15) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S266. Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 10(6Q15) MUTATED	166	66	45
DEL PEAK 10(6Q15) WILD-TYPE	247	150	150

Figure S266. Get High-res Image Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(6q27) mutation analysis' versus 'CN_CNMF'

P value = 3.04e-13 (Chi-square test), Q value = 1.5e-10

Table S267. Gene #39: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 11(6Q27) MUTATED	77	23	97	70	36
DEL PEAK 11(6Q27) WILD-TYPE	269	53	101	145	20

Figure S267. Get High-res Image Gene #39: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000233 (Fisher's exact test), Q value = 0.051

Table S268. Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 12(7P22.3) MUTATED	30	6	38
DEL PEAK 12(7P22.3) WILD-TYPE	226	86	121

Figure S268. Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000547 (Fisher's exact test), Q value = 0.11

Table S269. Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 12(7P22.3) MUTATED	27	39	8
DEL PEAK 12(7P22.3) WILD-TYPE	94	213	126

Figure S269. Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 12(7p22.3) mutation analysis' versus 'CN_CNMF'

P value = 7.09e-16 (Chi-square test), Q value = 3.7e-13

Table S270. Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 12(7P22.3) MUTATED	12	3	44	54	4
DEL PEAK 12(7P22.3) WILD-TYPE	334	73	154	161	52

Figure S270. Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.54e-05 (Chi-square test), Q value = 0.0042

Table S271. Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 12(7P22.3) MUTATED	22	7	12	17	2	2
DEL PEAK 12(7P22.3) WILD-TYPE	74	135	68	106	34	88

Figure S271. Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.93e-09 (Fisher's exact test), Q value = 3.1e-06

Table S272. Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 12(7P22.3) MUTATED	54	4	56
DEL PEAK 12(7P22.3) WILD-TYPE	181	151	378

Figure S272. Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.72e-06 (Fisher's exact test), Q value = 0.0011

Table S273. Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 12(7P22.3) MUTATED	59	12	43
DEL PEAK 12(7P22.3) WILD-TYPE	354	204	152

Figure S273. Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(7p22.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.9e-10 (Fisher's exact test), Q value = 1.6e-07

Table S274. Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 12(7P22.3) MUTATED	9	43	61
DEL PEAK 12(7P22.3) WILD-TYPE	191	380	188

Figure S274. Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.62e-09 (Fisher's exact test), Q value = 1.4e-06

Table S275. Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 12(7P22.3) MUTATED	51	50	12
DEL PEAK 12(7P22.3) WILD-TYPE	153	559	47

Figure S275. Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(7q36.1) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000562 (Fisher's exact test), Q value = 0.11

Table S276. Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 13(7Q36.1) MUTATED	43	11	48
DEL PEAK 13(7Q36.1) WILD-TYPE	213	81	111

Figure S276. Get High-res Image Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 13(7q36.1) mutation analysis' versus 'CN_CNMF'

P value = 2.34e-08 (Chi-square test), Q value = 8.7e-06

Table S277. Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 13(7Q36.1) MUTATED	39	13	56	61	4
DEL PEAK 13(7Q36.1) WILD-TYPE	307	63	142	154	52

Figure S277. Get High-res Image Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(7q36.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000824 (Fisher's exact test), Q value = 0.17

Table S278. Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 13(7Q36.1) MUTATED	65	19	85
DEL PEAK 13(7Q36.1) WILD-TYPE	170	136	349

Figure S278. Get High-res Image Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 13(7q36.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.75e-09 (Fisher's exact test), Q value = 3e-06

Table S279. Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 13(7Q36.1) MUTATED	22	65	80
DEL PEAK 13(7Q36.1) WILD-TYPE	178	358	169

Figure S279. Get High-res Image Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 13(7q36.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.57e-06 (Fisher's exact test), Q value = 5e-04

Table S280. Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 13(7Q36.1) MUTATED	55	90	22
DEL PEAK 13(7Q36.1) WILD-TYPE	149	519	37

Figure S280. Get High-res Image Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2) mutation analysis' versus 'MRNA_CNMF'

P value = 3.44e-05 (Fisher's exact test), Q value = 0.009

Table S281. Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 14(8P23.2) MUTATED	122	42	109
DEL PEAK 14(8P23.2) WILD-TYPE	134	50	50

Figure S281. Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 14(8p23.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.92e-06 (Fisher's exact test), Q value = 0.00089

Table S282. Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 14(8P23.2) MUTATED	85	136	52
DEL PEAK 14(8P23.2) WILD-TYPE	36	116	82

Figure S282. Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 14(8p23.2) mutation analysis' versus 'CN_CNMF'

P value = 1.15e-30 (Chi-square test), Q value = 6.9e-28

Table S283. Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 14(8P23.2) MUTATED	115	18	139	154	43
DEL PEAK 14(8P23.2) WILD-TYPE	231	58	59	61	13

Figure S283. Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 14(8p23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.92e-10 (Chi-square test), Q value = 1.2e-07

Table S284. Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 14(8P23.2) MUTATED	64	42	42	83	17	36
DEL PEAK 14(8P23.2) WILD-TYPE	32	100	38	40	19	54

Figure S284. Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 14(8p23.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.38e-11 (Fisher's exact test), Q value = 1.1e-08

Table S285. Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 14(8P23.2) MUTATED	160	50	230
DEL PEAK 14(8P23.2) WILD-TYPE	75	105	204

Figure S285. Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 14(8p23.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.01e-06 (Fisher's exact test), Q value = 0.00063

Table S286. Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 14(8P23.2) MUTATED	218	91	131
DEL PEAK 14(8P23.2) WILD-TYPE	195	125	64

Figure S286. Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.35e-08 (Fisher's exact test), Q value = 1.9e-05

Table S287. Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 14(8P23.2) MUTATED	86	203	168
DEL PEAK 14(8P23.2) WILD-TYPE	114	220	81

Figure S287. Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 14(8p23.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.5e-09 (Fisher's exact test), Q value = 6e-07

Table S288. Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 14(8P23.2) MUTATED	143	277	37
DEL PEAK 14(8P23.2) WILD-TYPE	61	332	22

Figure S288. Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(8p11.21) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000175 (Fisher's exact test), Q value = 0.039

Table S289. Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 15(8P11.21) MUTATED	34	18	48
DEL PEAK 15(8P11.21) WILD-TYPE	222	74	111

Figure S289. Get High-res Image Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 15(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 1.12e-10 (Chi-square test), Q value = 4.8e-08

Table S290. Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 15(8P11.21) MUTATED	40	9	50	69	2
DEL PEAK 15(8P11.21) WILD-TYPE	306	67	148	146	54

Figure S290. Get High-res Image Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 15(8p11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000996 (Fisher's exact test), Q value = 0.19

Table S291. Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 15(8P11.21) MUTATED	63	19	77
DEL PEAK 15(8P11.21) WILD-TYPE	172	136	357

Figure S291. Get High-res Image Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 15(8p11.21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.97e-06 (Fisher's exact test), Q value = 0.0014

Table S292. Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 15(8P11.21) MUTATED	57	91	20
DEL PEAK 15(8P11.21) WILD-TYPE	147	518	39

Figure S292. Get High-res Image Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0029

Table S293. Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 16(9P21.3) MUTATED	86	19	79
DEL PEAK 16(9P21.3) WILD-TYPE	170	73	80

Figure S293. Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 16(9p21.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.96e-06 (Fisher's exact test), Q value = 0.0012

Table S294. Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 16(9P21.3) MUTATED	43	114	27
DEL PEAK 16(9P21.3) WILD-TYPE	78	138	107

Figure S294. Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 16(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 7.63e-29 (Chi-square test), Q value = 4.6e-26

Table S295. Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 16(9P21.3) MUTATED	46	23	117	98	14
DEL PEAK 16(9P21.3) WILD-TYPE	300	53	81	117	42

Figure S295. Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 16(9p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.76e-14 (Chi-square test), Q value = 1.4e-11

Table S296. Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 16(9P21.3) MUTATED	39	17	34	64	7	13
DEL PEAK 16(9P21.3) WILD-TYPE	57	125	46	59	29	77

Figure S296. Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 16(9p21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.14e-07 (Fisher's exact test), Q value = 4e-05

Table S297. Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 16(9P21.3) MUTATED	94	25	167
DEL PEAK 16(9P21.3) WILD-TYPE	141	130	267

Figure S297. Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 16(9p21.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.58e-10 (Fisher's exact test), Q value = 3.9e-07

Table S298. Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 16(9P21.3) MUTATED	35	140	114
DEL PEAK 16(9P21.3) WILD-TYPE	165	283	135

Figure S298. Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 16(9p21.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.013

Table S299. Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 16(9P21.3) MUTATED	86	174	29
DEL PEAK 16(9P21.3) WILD-TYPE	118	435	30

Figure S299. Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(9q21.11) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000914 (Fisher's exact test), Q value = 0.18

Table S300. Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 17(9Q21.11) MUTATED	68	18	64
DEL PEAK 17(9Q21.11) WILD-TYPE	188	74	95

Figure S300. Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.0054

Table S301. Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 17(9Q21.11) MUTATED	47	83	20
DEL PEAK 17(9Q21.11) WILD-TYPE	74	169	114

Figure S301. Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 17(9q21.11) mutation analysis' versus 'CN_CNMF'

P value = 9.57e-18 (Chi-square test), Q value = 5.2e-15

Table S302. Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 17(9Q21.11) MUTATED	36	22	76	90	15
DEL PEAK 17(9Q21.11) WILD-TYPE	310	54	122	125	41

Figure S302. Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.77e-10 (Chi-square test), Q value = 4e-07

Table S303. Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 17(9Q21.11) MUTATED	37	13	17	49	4	16
DEL PEAK 17(9Q21.11) WILD-TYPE	59	129	63	74	32	74

Figure S303. Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'RPPA_CNMF'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.004

Table S304. Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 17(9Q21.11) MUTATED	64	32	21
DEL PEAK 17(9Q21.11) WILD-TYPE	82	97	94

Figure S304. Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.82e-06 (Fisher's exact test), Q value = 0.00086

Table S305. Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 17(9Q21.11) MUTATED	85	21	122
DEL PEAK 17(9Q21.11) WILD-TYPE	150	134	312

Figure S305. Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.67e-05 (Fisher's exact test), Q value = 0.021

Table S306. Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 17(9Q21.11) MUTATED	117	39	72
DEL PEAK 17(9Q21.11) WILD-TYPE	296	177	123

Figure S306. Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(9q21.11) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.68e-09 (Fisher's exact test), Q value = 3.3e-06

Table S307. Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 17(9Q21.11) MUTATED	31	101	100
DEL PEAK 17(9Q21.11) WILD-TYPE	169	322	149

Figure S307. Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.35e-09 (Fisher's exact test), Q value = 5.5e-07

Table S308. Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 17(9Q21.11) MUTATED	88	124	20
DEL PEAK 17(9Q21.11) WILD-TYPE	116	485	39

Figure S308. Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(10q23.31) mutation analysis' versus 'MRNA_CNMF'

P value = 4.65e-07 (Fisher's exact test), Q value = 0.00015

Table S309. Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 18(10Q23.31) MUTATED	51	23	71
DEL PEAK 18(10Q23.31) WILD-TYPE	205	69	88

Figure S309. Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.022

Table S310. Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 18(10Q23.31) MUTATED	53	65	27
DEL PEAK 18(10Q23.31) WILD-TYPE	68	187	107

Figure S310. Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 18(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 1.31e-18 (Chi-square test), Q value = 7.2e-16

Table S311. Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 18(10Q23.31) MUTATED	45	19	72	105	17
DEL PEAK 18(10Q23.31) WILD-TYPE	301	57	126	110	39

Figure S311. Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.14e-11 (Chi-square test), Q value = 2.3e-08

Table S312. Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 18(10Q23.31) MUTATED	51	19	26	48	7	16
DEL PEAK 18(10Q23.31) WILD-TYPE	45	123	54	75	29	74

Figure S312. Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'RPPA_CNMF'

P value = 5.69e-08 (Fisher's exact test), Q value = 2.1e-05

Table S313. Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 18(10Q23.31) MUTATED	67	30	17
DEL PEAK 18(10Q23.31) WILD-TYPE	79	99	98

Figure S313. Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.15e-05 (Fisher's exact test), Q value = 0.0058

Table S314. Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 18(10Q23.31) MUTATED	45	16	53
DEL PEAK 18(10Q23.31) WILD-TYPE	111	92	73

Figure S314. Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 18(10q23.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.38e-12 (Fisher's exact test), Q value = 1.1e-09

Table S315. Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 18(10Q23.31) MUTATED	109	21	114
DEL PEAK 18(10Q23.31) WILD-TYPE	126	134	320

Figure S315. Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.39e-08 (Fisher's exact test), Q value = 2.3e-05

Table S316. Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 18(10Q23.31) MUTATED	111	44	89
DEL PEAK 18(10Q23.31) WILD-TYPE	302	172	106

Figure S316. Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(10q23.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.41e-09 (Fisher's exact test), Q value = 1.7e-06

Table S317. Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 18(10Q23.31) MUTATED	41	99	109
DEL PEAK 18(10Q23.31) WILD-TYPE	159	324	140

Figure S317. Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.12e-09 (Fisher's exact test), Q value = 1.6e-06

Table S318. Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 18(10Q23.31) MUTATED	94	139	16
DEL PEAK 18(10Q23.31) WILD-TYPE	110	470	43

Figure S318. Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(10q26.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.75e-09 (Fisher's exact test), Q value = 7e-07

Table S319. Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 19(10Q26.3) MUTATED	49	23	77
DEL PEAK 19(10Q26.3) WILD-TYPE	207	69	82

Figure S319. Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.68e-07 (Fisher's exact test), Q value = 0.00012

Table S320. Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 19(10Q26.3) MUTATED	58	68	23
DEL PEAK 19(10Q26.3) WILD-TYPE	63	184	111

Figure S320. Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(10q26.3) mutation analysis' versus 'CN_CNMF'

P value = 1.02e-19 (Chi-square test), Q value = 5.7e-17

Table S321. Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 19(10Q26.3) MUTATED	46	17	72	108	16
DEL PEAK 19(10Q26.3) WILD-TYPE	300	59	126	107	40

Figure S321. Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.24e-10 (Chi-square test), Q value = 5.4e-08

Table S322. Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 19(10Q26.3) MUTATED	51	18	31	40	8	17
DEL PEAK 19(10Q26.3) WILD-TYPE	45	124	49	83	28	73

Figure S322. Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'RPPA_CNMF'

P value = 2.12e-08 (Fisher's exact test), Q value = 8e-06

Table S323. Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 19(10Q26.3) MUTATED	71	26	22
DEL PEAK 19(10Q26.3) WILD-TYPE	75	103	93

Figure S323. Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.92e-07 (Fisher's exact test), Q value = 6.7e-05

Table S324. Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 19(10Q26.3) MUTATED	43	16	60
DEL PEAK 19(10Q26.3) WILD-TYPE	113	92	66

Figure S324. Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(10q26.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.56e-15 (Fisher's exact test), Q value = 8.1e-13

Table S325. Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 19(10Q26.3) MUTATED	114	18	112
DEL PEAK 19(10Q26.3) WILD-TYPE	121	137	322

Figure S325. Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-10 (Fisher's exact test), Q value = 9.6e-08

Table S326. Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 19(10Q26.3) MUTATED	112	39	93
DEL PEAK 19(10Q26.3) WILD-TYPE	301	177	102

Figure S326. Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(10q26.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.66e-13 (Fisher's exact test), Q value = 8e-11

Table S327. Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 19(10Q26.3) MUTATED	39	91	118
DEL PEAK 19(10Q26.3) WILD-TYPE	161	332	131

Figure S327. Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.91e-12 (Fisher's exact test), Q value = 9e-10

Table S328. Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 19(10Q26.3) MUTATED	96	128	24
DEL PEAK 19(10Q26.3) WILD-TYPE	108	481	35

Figure S328. Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(11p15.5) mutation analysis' versus 'MRNA_CNMF'

P value = 5.04e-11 (Fisher's exact test), Q value = 2.2e-08

Table S329. Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 20(11P15.5) MUTATED	47	24	80
DEL PEAK 20(11P15.5) WILD-TYPE	209	68	79

Figure S329. Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.22e-08 (Fisher's exact test), Q value = 2.2e-05

Table S330. Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 20(11P15.5) MUTATED	62	60	29
DEL PEAK 20(11P15.5) WILD-TYPE	59	192	105

Figure S330. Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 20(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 3e-30 (Chi-square test), Q value = 1.8e-27

Table S331. Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 20(11P15.5) MUTATED	40	14	68	124	13
DEL PEAK 20(11P15.5) WILD-TYPE	306	62	130	91	43

Figure S331. Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.01e-09 (Chi-square test), Q value = 4.1e-07

Table S332. Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 20(11P15.5) MUTATED	48	16	26	38	10	15
DEL PEAK 20(11P15.5) WILD-TYPE	48	126	54	85	26	75

Figure S332. Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'RPPA_CNMF'

P value = 2.51e-09 (Fisher's exact test), Q value = 1e-06

Table S333. Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 20(11P15.5) MUTATED	76	26	25
DEL PEAK 20(11P15.5) WILD-TYPE	70	103	90

Figure S333. Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 3.81e-06 (Fisher's exact test), Q value = 0.0011

Table S334. Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 20(11P15.5) MUTATED	38	26	63
DEL PEAK 20(11P15.5) WILD-TYPE	118	82	63

Figure S334. Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 20(11p15.5) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.05e-16 (Fisher's exact test), Q value = 5.6e-14

Table S335. Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 20(11P15.5) MUTATED	119	22	102
DEL PEAK 20(11P15.5) WILD-TYPE	116	133	332

Figure S335. Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.64e-12 (Fisher's exact test), Q value = 1.7e-09

Table S336. Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 20(11P15.5) MUTATED	97	47	99
DEL PEAK 20(11P15.5) WILD-TYPE	316	169	96

Figure S336. Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(11p15.5) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.33e-17 (Fisher's exact test), Q value = 3.9e-14

Table S337. Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 20(11P15.5) MUTATED	38	88	125
DEL PEAK 20(11P15.5) WILD-TYPE	162	335	124

Figure S337. Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.13e-17 (Fisher's exact test), Q value = 3.8e-14

Table S338. Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 20(11P15.5) MUTATED	106	123	22
DEL PEAK 20(11P15.5) WILD-TYPE	98	486	37

Figure S338. Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 21(11q23.2) mutation analysis' versus 'CN_CNMF'

P value = 3.59e-26 (Chi-square test), Q value = 2.1e-23

Table S339. Gene #49: 'Del Peak 21(11q23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 21(11Q23.2) MUTATED	117	33	164	106	22
DEL PEAK 21(11Q23.2) WILD-TYPE	229	43	34	109	34

Figure S339. Get High-res Image Gene #49: 'Del Peak 21(11q23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 21(11q23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.17e-10 (Chi-square test), Q value = 1.3e-07

Table S340. Gene #49: 'Del Peak 21(11q23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 21(11Q23.2) MUTATED	36	57	51	90	20	31
DEL PEAK 21(11Q23.2) WILD-TYPE	60	85	29	33	16	59

Figure S340. Get High-res Image Gene #49: 'Del Peak 21(11q23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 22(12p13.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000962 (Fisher's exact test), Q value = 0.19

Table S341. Gene #50: 'Del Peak 22(12p13.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 22(12P13.1) MUTATED	30	60	63
DEL PEAK 22(12P13.1) WILD-TYPE	170	363	186

Figure S341. Get High-res Image Gene #50: 'Del Peak 22(12p13.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 22(12p13.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.45e-05 (Fisher's exact test), Q value = 0.022

Table S342. Gene #50: 'Del Peak 22(12p13.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 22(12P13.1) MUTATED	50	85	18
DEL PEAK 22(12P13.1) WILD-TYPE	154	524	41

Figure S342. Get High-res Image Gene #50: 'Del Peak 22(12p13.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 23(12q24.31) mutation analysis' versus 'MRNA_CNMF'

P value = 1.7e-10 (Fisher's exact test), Q value = 7.3e-08

Table S343. Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 23(12Q24.31) MUTATED	21	22	54
DEL PEAK 23(12Q24.31) WILD-TYPE	235	70	105

Figure S343. Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.29e-11 (Fisher's exact test), Q value = 4.1e-08

Table S344. Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 23(12Q24.31) MUTATED	50	34	13
DEL PEAK 23(12Q24.31) WILD-TYPE	71	218	121

Figure S344. Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 23(12q24.31) mutation analysis' versus 'CN_CNMF'

P value = 1.9e-19 (Chi-square test), Q value = 1.1e-16

Table S345. Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 23(12Q24.31) MUTATED	34	13	20	86	9
DEL PEAK 23(12Q24.31) WILD-TYPE	312	63	178	129	47

Figure S345. Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.87e-13 (Chi-square test), Q value = 1.4e-10

Table S346. Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 23(12Q24.31) MUTATED	43	10	14	14	4	11
DEL PEAK 23(12Q24.31) WILD-TYPE	53	132	66	109	32	79

Figure S346. Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'RPPA_CNMF'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.004

Table S347. Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 23(12Q24.31) MUTATED	46	12	19
DEL PEAK 23(12Q24.31) WILD-TYPE	100	117	96

Figure S347. Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 7.16e-07 (Fisher's exact test), Q value = 0.00023

Table S348. Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 23(12Q24.31) MUTATED	20	12	45
DEL PEAK 23(12Q24.31) WILD-TYPE	136	96	81

Figure S348. Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 23(12q24.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.91e-17 (Fisher's exact test), Q value = 3.7e-14

Table S349. Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 23(12Q24.31) MUTATED	85	17	41
DEL PEAK 23(12Q24.31) WILD-TYPE	150	138	393

Figure S349. Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.16e-16 (Fisher's exact test), Q value = 1.1e-13

Table S350. Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 23(12Q24.31) MUTATED	39	29	75
DEL PEAK 23(12Q24.31) WILD-TYPE	374	187	120

Figure S350. Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 23(12q24.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.28e-12 (Fisher's exact test), Q value = 1.5e-09

Table S351. Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 23(12Q24.31) MUTATED	29	45	83
DEL PEAK 23(12Q24.31) WILD-TYPE	171	378	166

Figure S351. Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.24e-12 (Fisher's exact test), Q value = 1.5e-09

Table S352. Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 23(12Q24.31) MUTATED	69	71	17
DEL PEAK 23(12Q24.31) WILD-TYPE	135	538	42

Figure S352. Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 24(13q14.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.0081

Table S353. Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 24(13Q14.2) MUTATED	74	120	44
DEL PEAK 24(13Q14.2) WILD-TYPE	47	132	90

Figure S353. Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 24(13q14.2) mutation analysis' versus 'CN_CNMF'

P value = 2.43e-28 (Chi-square test), Q value = 1.5e-25

Table S354. Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 24(13Q14.2) MUTATED	74	46	126	126	35
DEL PEAK 24(13Q14.2) WILD-TYPE	272	30	72	89	21

Figure S354. Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 24(13q14.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.51e-06 (Chi-square test), Q value = 0.00077

Table S355. Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 24(13Q14.2) MUTATED	58	48	47	64	11	29
DEL PEAK 24(13Q14.2) WILD-TYPE	38	94	33	59	25	61

Figure S355. Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 24(13q14.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.34e-07 (Fisher's exact test), Q value = 4.7e-05

Table S356. Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 24(13Q14.2) MUTATED	134	44	205
DEL PEAK 24(13Q14.2) WILD-TYPE	101	111	229

Figure S356. Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 24(13q14.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.45e-05 (Fisher's exact test), Q value = 0.009

Table S357. Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 24(13Q14.2) MUTATED	193	77	113
DEL PEAK 24(13Q14.2) WILD-TYPE	220	139	82

Figure S357. Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 24(13q14.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.55e-08 (Fisher's exact test), Q value = 5.9e-06

Table S358. Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 24(13Q14.2) MUTATED	61	189	146
DEL PEAK 24(13Q14.2) WILD-TYPE	139	234	103

Figure S358. Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 24(13q14.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.62e-05 (Fisher's exact test), Q value = 0.007

Table S359. Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 24(13Q14.2) MUTATED	114	246	36
DEL PEAK 24(13Q14.2) WILD-TYPE	90	363	23

Figure S359. Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(14q24.3) mutation analysis' versus 'MRNA_CNMF'

P value = 2.58e-07 (Fisher's exact test), Q value = 8.8e-05

Table S360. Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 25(14Q24.3) MUTATED	60	28	79
DEL PEAK 25(14Q24.3) WILD-TYPE	196	64	80

Figure S360. Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.05e-09 (Fisher's exact test), Q value = 4.3e-07

Table S361. Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 25(14Q24.3) MUTATED	69	69	29
DEL PEAK 25(14Q24.3) WILD-TYPE	52	183	105

Figure S361. Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 25(14q24.3) mutation analysis' versus 'CN_CNMF'

P value = 6.75e-33 (Chi-square test), Q value = 4.1e-30

Table S362. Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 25(14Q24.3) MUTATED	42	17	72	133	22
DEL PEAK 25(14Q24.3) WILD-TYPE	304	59	126	82	34

Figure S362. Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.58e-13 (Chi-square test), Q value = 2.2e-10

Table S363. Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 25(14Q24.3) MUTATED	55	16	27	48	7	20
DEL PEAK 25(14Q24.3) WILD-TYPE	41	126	53	75	29	70

Figure S363. Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'RPPA_CNMF'

P value = 2.51e-07 (Fisher's exact test), Q value = 8.6e-05

Table S364. Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 25(14Q24.3) MUTATED	74	28	29
DEL PEAK 25(14Q24.3) WILD-TYPE	72	101	86

Figure S364. Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.89e-06 (Fisher's exact test), Q value = 0.00088

Table S365. Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 25(14Q24.3) MUTATED	44	23	64
DEL PEAK 25(14Q24.3) WILD-TYPE	112	85	62

Figure S365. Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 25(14q24.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.99e-14 (Fisher's exact test), Q value = 9.9e-12

Table S366. Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 25(14Q24.3) MUTATED	122	25	121
DEL PEAK 25(14Q24.3) WILD-TYPE	113	130	313

Figure S366. Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.1e-12 (Fisher's exact test), Q value = 5.2e-10

Table S367. Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 25(14Q24.3) MUTATED	114	48	106
DEL PEAK 25(14Q24.3) WILD-TYPE	299	168	89

Figure S367. Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(14q24.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.25e-18 (Fisher's exact test), Q value = 4.5e-15

Table S368. Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 25(14Q24.3) MUTATED	46	95	135
DEL PEAK 25(14Q24.3) WILD-TYPE	154	328	114

Figure S368. Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.23e-20 (Fisher's exact test), Q value = 7e-18

Table S369. Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 25(14Q24.3) MUTATED	119	134	23
DEL PEAK 25(14Q24.3) WILD-TYPE	85	475	36

Figure S369. Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(15q13.1) mutation analysis' versus 'MRNA_CNMF'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.00066

Table S370. Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 26(15Q13.1) MUTATED	75	28	85
DEL PEAK 26(15Q13.1) WILD-TYPE	181	64	74

Figure S370. Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.26e-08 (Fisher's exact test), Q value = 1.2e-05

Table S371. Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 26(15Q13.1) MUTATED	68	92	28
DEL PEAK 26(15Q13.1) WILD-TYPE	53	160	106

Figure S371. Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 26(15q13.1) mutation analysis' versus 'CN_CNMF'

P value = 9.29e-31 (Chi-square test), Q value = 5.6e-28

Table S372. Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 26(15Q13.1) MUTATED	52	37	69	137	15
DEL PEAK 26(15Q13.1) WILD-TYPE	294	39	129	78	41

Figure S372. Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.25e-12 (Chi-square test), Q value = 2.4e-09

Table S373. Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 26(15Q13.1) MUTATED	60	23	27	48	8	23
DEL PEAK 26(15Q13.1) WILD-TYPE	36	119	53	75	28	67

Figure S373. Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000316 (Fisher's exact test), Q value = 0.068

Table S374. Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 26(15Q13.1) MUTATED	76	39	38
DEL PEAK 26(15Q13.1) WILD-TYPE	70	90	77

Figure S374. Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.78e-05 (Fisher's exact test), Q value = 0.012

Table S375. Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 26(15Q13.1) MUTATED	54	30	69
DEL PEAK 26(15Q13.1) WILD-TYPE	102	78	57

Figure S375. Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 26(15q13.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.27e-15 (Fisher's exact test), Q value = 1.7e-12

Table S376. Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 26(15Q13.1) MUTATED	127	24	138
DEL PEAK 26(15Q13.1) WILD-TYPE	108	131	296

Figure S376. Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-12 (Fisher's exact test), Q value = 6.7e-10

Table S377. Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 26(15Q13.1) MUTATED	126	52	111
DEL PEAK 26(15Q13.1) WILD-TYPE	287	164	84

Figure S377. Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(15q13.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.02e-15 (Fisher's exact test), Q value = 5.3e-13

Table S378. Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 26(15Q13.1) MUTATED	40	124	137
DEL PEAK 26(15Q13.1) WILD-TYPE	160	299	112

Figure S378. Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.67e-21 (Fisher's exact test), Q value = 1.5e-18

Table S379. Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 26(15Q13.1) MUTATED	119	147	35
DEL PEAK 26(15Q13.1) WILD-TYPE	85	462	24

Figure S379. Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(16q24.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.76e-12 (Fisher's exact test), Q value = 8.3e-10

Table S380. Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 27(16Q24.3) MUTATED	204	57	71
DEL PEAK 27(16Q24.3) WILD-TYPE	52	35	88

Figure S380. Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.68e-13 (Fisher's exact test), Q value = 2.7e-10

Table S381. Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 27(16Q24.3) MUTATED	45	181	106
DEL PEAK 27(16Q24.3) WILD-TYPE	76	71	28

Figure S381. Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 27(16q24.3) mutation analysis' versus 'CN_CNMF'

P value = 6.56e-11 (Chi-square test), Q value = 2.9e-08

Table S382. Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 27(16Q24.3) MUTATED	245	61	132	96	41
DEL PEAK 27(16Q24.3) WILD-TYPE	101	15	66	119	15

Figure S382. Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.16e-10 (Chi-square test), Q value = 1.7e-07

Table S383. Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 27(16Q24.3) MUTATED	40	119	59	71	19	57
DEL PEAK 27(16Q24.3) WILD-TYPE	56	23	21	52	17	33

Figure S383. Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'RPPA_CNMF'

P value = 1.71e-09 (Fisher's exact test), Q value = 6.9e-07

Table S384. Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 27(16Q24.3) MUTATED	63	100	83
DEL PEAK 27(16Q24.3) WILD-TYPE	83	29	32

Figure S384. Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.08e-11 (Fisher's exact test), Q value = 9.4e-09

Table S385. Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 27(16Q24.3) MUTATED	116	82	48
DEL PEAK 27(16Q24.3) WILD-TYPE	40	26	78

Figure S385. Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 27(16q24.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.34e-18 (Fisher's exact test), Q value = 1.8e-15

Table S386. Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 27(16Q24.3) MUTATED	97	123	314
DEL PEAK 27(16Q24.3) WILD-TYPE	138	32	120

Figure S386. Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.19e-17 (Fisher's exact test), Q value = 6.5e-15

Table S387. Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 27(16Q24.3) MUTATED	301	159	74
DEL PEAK 27(16Q24.3) WILD-TYPE	112	57	121

Figure S387. Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(16q24.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.67e-14 (Fisher's exact test), Q value = 2.8e-11

Table S388. Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 27(16Q24.3) MUTATED	134	317	112
DEL PEAK 27(16Q24.3) WILD-TYPE	66	106	137

Figure S388. Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-20 (Fisher's exact test), Q value = 1.1e-17

Table S389. Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 27(16Q24.3) MUTATED	78	454	31
DEL PEAK 27(16Q24.3) WILD-TYPE	126	155	28

Figure S389. Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(17p12) mutation analysis' versus 'MRNA_CNMF'

P value = 4.01e-06 (Fisher's exact test), Q value = 0.0012

Table S390. Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 28(17P12) MUTATED	133	55	121
DEL PEAK 28(17P12) WILD-TYPE	123	37	38

Figure S390. Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 28(17p12) mutation analysis' versus 'CN_CNMF'

P value = 1.35e-21 (Chi-square test), Q value = 7.8e-19

Table S391. Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 28(17P12) MUTATED	146	37	154	167	33
DEL PEAK 28(17P12) WILD-TYPE	200	39	44	48	23

Figure S391. Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 28(17p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.15e-07 (Chi-square test), Q value = 7.4e-05

Table S392. Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 28(17P12) MUTATED	59	63	60	94	20	46
DEL PEAK 28(17P12) WILD-TYPE	37	79	20	29	16	44

Figure S392. Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 28(17p12) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000114 (Fisher's exact test), Q value = 0.026

Table S393. Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 28(17P12) MUTATED	108	65	64
DEL PEAK 28(17P12) WILD-TYPE	38	64	51

Figure S393. Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 28(17p12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.00047

Table S394. Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 28(17P12) MUTATED	110	234	184
DEL PEAK 28(17P12) WILD-TYPE	90	189	65

Figure S394. Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 28(17p12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.81e-06 (Fisher's exact test), Q value = 0.00057

Table S395. Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 28(17P12) MUTATED	141	338	49
DEL PEAK 28(17P12) WILD-TYPE	63	271	10

Figure S395. Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(17q21.31) mutation analysis' versus 'MRNA_CNMF'

P value = 2.35e-12 (Fisher's exact test), Q value = 1.1e-09

Table S396. Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 29(17Q21.31) MUTATED	60	36	94
DEL PEAK 29(17Q21.31) WILD-TYPE	196	56	65

Figure S396. Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.82e-07 (Fisher's exact test), Q value = 0.00013

Table S397. Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 29(17Q21.31) MUTATED	71	78	41
DEL PEAK 29(17Q21.31) WILD-TYPE	50	174	93

Figure S397. Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 29(17q21.31) mutation analysis' versus 'CN_CNMF'

P value = 9.31e-23 (Chi-square test), Q value = 5.4e-20

Table S398. Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 29(17Q21.31) MUTATED	80	17	66	137	12
DEL PEAK 29(17Q21.31) WILD-TYPE	266	59	132	78	44

Figure S398. Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.98e-14 (Chi-square test), Q value = 2.5e-11

Table S399. Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 29(17Q21.31) MUTATED	60	16	33	38	10	29
DEL PEAK 29(17Q21.31) WILD-TYPE	36	126	47	85	26	61

Figure S399. Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'RPPA_CNMF'

P value = 1.55e-11 (Fisher's exact test), Q value = 7e-09

Table S400. Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 29(17Q21.31) MUTATED	87	24	44
DEL PEAK 29(17Q21.31) WILD-TYPE	59	105	71

Figure S400. Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 5.88e-11 (Fisher's exact test), Q value = 2.6e-08

Table S401. Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 29(17Q21.31) MUTATED	41	33	81
DEL PEAK 29(17Q21.31) WILD-TYPE	115	75	45

Figure S401. Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 29(17q21.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.21e-20 (Fisher's exact test), Q value = 6.9e-18

Table S402. Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 29(17Q21.31) MUTATED	144	41	109
DEL PEAK 29(17Q21.31) WILD-TYPE	91	114	325

Figure S402. Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-15 (Fisher's exact test), Q value = 6.1e-13

Table S403. Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 29(17Q21.31) MUTATED	100	79	115
DEL PEAK 29(17Q21.31) WILD-TYPE	313	137	80

Figure S403. Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(17q21.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.78e-14 (Fisher's exact test), Q value = 8.9e-12

Table S404. Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 29(17Q21.31) MUTATED	59	108	138
DEL PEAK 29(17Q21.31) WILD-TYPE	141	315	111

Figure S404. Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.77e-16 (Fisher's exact test), Q value = 1.5e-13

Table S405. Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 29(17Q21.31) MUTATED	112	158	35
DEL PEAK 29(17Q21.31) WILD-TYPE	92	451	24

Figure S405. Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(18q23) mutation analysis' versus 'MRNA_CNMF'

P value = 6.04e-06 (Fisher's exact test), Q value = 0.0017

Table S406. Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 30(18Q23) MUTATED	67	22	76
DEL PEAK 30(18Q23) WILD-TYPE	189	70	83

Figure S406. Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 30(18q23) mutation analysis' versus 'CN_CNMF'

P value = 3.87e-12 (Chi-square test), Q value = 1.8e-09

Table S407. Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 30(18Q23) MUTATED	63	30	82	99	16
DEL PEAK 30(18Q23) WILD-TYPE	283	46	116	116	40

Figure S407. Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 30(18q23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.02e-08 (Chi-square test), Q value = 3.9e-06

Table S408. Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 30(18Q23) MUTATED	38	28	45	53	9	18
DEL PEAK 30(18Q23) WILD-TYPE	58	114	35	70	27	72

Figure S408. Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 30(18q23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.74e-05 (Fisher's exact test), Q value = 0.0073

Table S409. Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 30(18Q23) MUTATED	102	34	134
DEL PEAK 30(18Q23) WILD-TYPE	133	121	300

Figure S409. Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 30(18q23) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.011

Table S410. Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 30(18Q23) MUTATED	48	131	108
DEL PEAK 30(18Q23) WILD-TYPE	152	292	141

Figure S410. Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 30(18q23) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000169 (Fisher's exact test), Q value = 0.038

Table S411. Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 30(18Q23) MUTATED	86	174	27
DEL PEAK 30(18Q23) WILD-TYPE	118	435	32

Figure S411. Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(19p13.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.08e-09 (Fisher's exact test), Q value = 4.4e-07

Table S412. Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 31(19P13.3) MUTATED	69	24	90
DEL PEAK 31(19P13.3) WILD-TYPE	187	68	69

Figure S412. Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.68e-09 (Fisher's exact test), Q value = 3.7e-06

Table S413. Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 31(19P13.3) MUTATED	65	94	24
DEL PEAK 31(19P13.3) WILD-TYPE	56	158	110

Figure S413. Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 31(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 3.97e-43 (Chi-square test), Q value = 2.5e-40

Table S414. Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 31(19P13.3) MUTATED	32	13	108	128	20
DEL PEAK 31(19P13.3) WILD-TYPE	314	63	90	87	36

Figure S414. Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.05e-17 (Chi-square test), Q value = 2.2e-14

Table S415. Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 31(19P13.3) MUTATED	49	10	22	63	6	22
DEL PEAK 31(19P13.3) WILD-TYPE	47	132	58	60	30	68

Figure S415. Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'RPPA_CNMF'

P value = 2.67e-06 (Fisher's exact test), Q value = 0.00082

Table S416. Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 31(19P13.3) MUTATED	79	38	31
DEL PEAK 31(19P13.3) WILD-TYPE	67	91	84

Figure S416. Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.011

Table S417. Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 31(19P13.3) MUTATED	49	31	68
DEL PEAK 31(19P13.3) WILD-TYPE	107	77	58

Figure S417. Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 31(19p13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.11e-13 (Fisher's exact test), Q value = 1.5e-10

Table S418. Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 31(19P13.3) MUTATED	120	23	143
DEL PEAK 31(19P13.3) WILD-TYPE	115	132	291

Figure S418. Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.3e-09 (Fisher's exact test), Q value = 9.2e-07

Table S419. Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 31(19P13.3) MUTATED	139	47	100
DEL PEAK 31(19P13.3) WILD-TYPE	274	169	95

Figure S419. Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(19p13.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.07e-16 (Fisher's exact test), Q value = 4.7e-13

Table S420. Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 31(19P13.3) MUTATED	40	117	135
DEL PEAK 31(19P13.3) WILD-TYPE	160	306	114

Figure S420. Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.14e-14 (Fisher's exact test), Q value = 1.1e-11

Table S421. Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 31(19P13.3) MUTATED	113	154	25
DEL PEAK 31(19P13.3) WILD-TYPE	91	455	34

Figure S421. Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(19q13.32) mutation analysis' versus 'MRNA_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.0081

Table S422. Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	256	92	159
DEL PEAK 32(19Q13.32) MUTATED	34	12	49
DEL PEAK 32(19Q13.32) WILD-TYPE	222	80	110

Figure S422. Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 8.29e-06 (Fisher's exact test), Q value = 0.0024

Table S423. Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 32(19Q13.32) MUTATED	35	51	9
DEL PEAK 32(19Q13.32) WILD-TYPE	86	201	125

Figure S423. Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 32(19q13.32) mutation analysis' versus 'CN_CNMF'

P value = 1.77e-17 (Chi-square test), Q value = 9.6e-15

Table S424. Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 32(19Q13.32) MUTATED	23	8	66	69	14
DEL PEAK 32(19Q13.32) WILD-TYPE	323	68	132	146	42

Figure S424. Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.07e-11 (Chi-square test), Q value = 1.4e-08

Table S425. Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 32(19Q13.32) MUTATED	37	5	20	39	4	13
DEL PEAK 32(19Q13.32) WILD-TYPE	59	137	60	84	32	77

Figure S425. Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000469 (Fisher's exact test), Q value = 0.099

Table S426. Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 32(19Q13.32) MUTATED	44	18	15
DEL PEAK 32(19Q13.32) WILD-TYPE	102	111	100

Figure S426. Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.52e-05 (Fisher's exact test), Q value = 0.011

Table S427. Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	108	126
DEL PEAK 32(19Q13.32) MUTATED	25	11	41
DEL PEAK 32(19Q13.32) WILD-TYPE	131	97	85

Figure S427. Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 32(19q13.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.4e-09 (Fisher's exact test), Q value = 1.7e-06

Table S428. Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 32(19Q13.32) MUTATED	77	12	83
DEL PEAK 32(19Q13.32) WILD-TYPE	158	143	351

Figure S428. Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.39e-06 (Fisher's exact test), Q value = 0.00044

Table S429. Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 32(19Q13.32) MUTATED	86	24	62
DEL PEAK 32(19Q13.32) WILD-TYPE	327	192	133

Figure S429. Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(19q13.32) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.37e-10 (Fisher's exact test), Q value = 5.9e-08

Table S430. Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 32(19Q13.32) MUTATED	21	66	85
DEL PEAK 32(19Q13.32) WILD-TYPE	179	357	164

Figure S430. Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.46e-08 (Fisher's exact test), Q value = 9.2e-06

Table S431. Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 32(19Q13.32) MUTATED	59	89	24
DEL PEAK 32(19Q13.32) WILD-TYPE	145	520	35

Figure S431. Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(20p13) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.004

Table S432. Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	252	134
DEL PEAK 33(20P13) MUTATED	33	37	8
DEL PEAK 33(20P13) WILD-TYPE	88	215	126

Figure S432. Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 33(20p13) mutation analysis' versus 'CN_CNMF'

P value = 9.52e-14 (Chi-square test), Q value = 4.6e-11

Table S433. Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 33(20P13) MUTATED	18	4	36	61	13
DEL PEAK 33(20P13) WILD-TYPE	328	72	162	154	43

Figure S433. Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 33(20p13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.97e-07 (Chi-square test), Q value = 0.00013

Table S434. Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 33(20P13) MUTATED	28	5	11	22	3	7
DEL PEAK 33(20P13) WILD-TYPE	68	137	69	101	33	83

Figure S434. Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 33(20p13) mutation analysis' versus 'RPPA_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.17

Table S435. Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	129	115
DEL PEAK 33(20P13) MUTATED	35	10	16
DEL PEAK 33(20P13) WILD-TYPE	111	119	99

Figure S435. Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 33(20p13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.8e-10 (Fisher's exact test), Q value = 7.7e-08

Table S436. Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	155	434
DEL PEAK 33(20P13) MUTATED	64	6	55
DEL PEAK 33(20P13) WILD-TYPE	171	149	379

Figure S436. Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 33(20p13) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.57e-08 (Fisher's exact test), Q value = 9.5e-06

Table S437. Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	413	216	195
DEL PEAK 33(20P13) MUTATED	54	16	55
DEL PEAK 33(20P13) WILD-TYPE	359	200	140

Figure S437. Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(20p13) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.06e-11 (Fisher's exact test), Q value = 4.8e-09

Table S438. Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	200	423	249
DEL PEAK 33(20P13) MUTATED	15	39	70
DEL PEAK 33(20P13) WILD-TYPE	185	384	179

Figure S438. Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 33(20p13) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.74e-09 (Fisher's exact test), Q value = 7e-07

Table S439. Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	204	609	59
DEL PEAK 33(20P13) MUTATED	57	57	10
DEL PEAK 33(20P13) WILD-TYPE	147	552	49

Figure S439. Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(21q11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.38e-12 (Chi-square test), Q value = 6.5e-10

Table S440. Gene #62: 'Del Peak 34(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 34(21Q11.2) MUTATED	30	13	70	56	12
DEL PEAK 34(21Q11.2) WILD-TYPE	316	63	128	159	44

Figure S440. Get High-res Image Gene #62: 'Del Peak 34(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 34(21q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000275 (Chi-square test), Q value = 0.06

Table S441. Gene #62: 'Del Peak 34(21q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	96	142	80	123	36	90
DEL PEAK 34(21Q11.2) MUTATED	17	19	19	41	6	10
DEL PEAK 34(21Q11.2) WILD-TYPE	79	123	61	82	30	80

Figure S441. Get High-res Image Gene #62: 'Del Peak 34(21q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 35(22q13.32) mutation analysis' versus 'CN_CNMF'

P value = 0.000936 (Chi-square test), Q value = 0.18

Table S442. Gene #63: 'Del Peak 35(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	346	76	198	215	56
DEL PEAK 35(22Q13.32) MUTATED	130	46	102	95	26
DEL PEAK 35(22Q13.32) WILD-TYPE	216	30	96	120	30

Figure S442. Get High-res Image Gene #63: 'Del Peak 35(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 891
Number of copy number variation regions = 63
Number of molecular subtypes = 10
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

[4] GISTIC_version2

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